From 5ce762646c56189fb0c83016c3c074e3525186f1 Mon Sep 17 00:00:00 2001 From: DianaSpurite <112383244+DianaSpurite@users.noreply.github.com> Date: Tue, 8 Nov 2022 13:23:30 +0100 Subject: [PATCH 01/16] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5e0ac7190..fa59688d9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,8 @@ and this project follows to [Calendar Versioning](https://calver.org/). - Guellil 2022 10.1186/s13059-021-02580-z - Spyrou 2022 10.1038/s41586-022-04800-3 - Neumann 2022 10.1016/j.cub.2022.06.094 +- White 2021 10.3390/biology10121324 + #### Ancient Metagenome: Environmental From 134fa4dab5fdb3243483499db8bc8c46c56311bf Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 9 Dec 2022 14:09:40 +0100 Subject: [PATCH 02/16] Update check_dataset.yml --- .github/workflows/check_dataset.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check_dataset.yml b/.github/workflows/check_dataset.yml index 881dbb4c3..fa8dea31f 100644 --- a/.github/workflows/check_dataset.yml +++ b/.github/workflows/check_dataset.yml @@ -9,7 +9,7 @@ jobs: - uses: actions/checkout@v2 - uses: actions/setup-python@v1 with: - python-version: "3.6" + python-version: "3.9" architecture: "x64" - name: Install dependencies run: | From 5d785352850d8872a1a3391714fb0386391ade83 Mon Sep 17 00:00:00 2001 From: DianaSpurite <112383244+DianaSpurite@users.noreply.github.com> Date: Tue, 2 May 2023 18:44:24 +0200 Subject: [PATCH 03/16] Update ancientmetagenome-hostassociated_samples.tsv adding White 2021 samples --- ...ncientmetagenome-hostassociated_samples.tsv | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv b/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv index dffba8e35..0dca18f57 100644 --- a/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv +++ b/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv @@ -1066,3 +1066,21 @@ Modi2021 2021 10.1016/j.quaint.2021.12.003 Ponte San Pietro (Ischia di Castro) 4 Modi2021 2021 10.1016/j.quaint.2021.12.003 Ponte San Pietro (Ischia di Castro) 42.527 11.601 Italy PsP_6408 Homo sapiens 3400 10.1016/j.quaint.2021.12.003 oral dental calculus SRA PRJNA739881 SRS9263822 Modi2021 2021 10.1016/j.quaint.2021.12.003 Ponte San Pietro (Ischia di Castro) 42.527 11.601 Italy PsP_6407 Homo sapiens 3400 10.1016/j.quaint.2021.12.003 oral dental calculus SRA PRJNA739881 SRS9263817 Modi2021 2021 10.1016/j.quaint.2021.12.003 Ponte San Pietro (Ischia di Castro) 42.527 11.601 Italy PsP_6405 Homo sapiens 3400 10.1016/j.quaint.2021.12.003 oral dental calculus SRA PRJNA739881 SRS9263816 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769379 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B3 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769380 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B5 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769381 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B6 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769382 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B7 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769383 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769379 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769379 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B3 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769380 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B5 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769381 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B6 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769382 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B7 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769383 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769379 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769379 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B3 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769380 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B5 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769381 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B6 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769382 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B7 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769383 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769379 From a82ef280e73d0c96e0b1e6ed4ada52fdc3bb22dc Mon Sep 17 00:00:00 2001 From: DianaSpurite <112383244+DianaSpurite@users.noreply.github.com> Date: Tue, 2 May 2023 18:45:21 +0200 Subject: [PATCH 04/16] Update ancientmetagenome-hostassociated_libraries.tsv adding White 2021 libraries --- .../ancientmetagenome-hostassociated_libraries.tsv | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv b/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv index bcdf6083f..a4232e435 100644 --- a/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv +++ b/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv @@ -1834,3 +1834,11 @@ Modi2021 2021 10.1016/j.quaint.2021.12.003 PsP_6410 SRA PRJNA739881 SRS9263818 6 Modi2021 2021 10.1016/j.quaint.2021.12.003 PsP_6408 SRA PRJNA739881 SRS9263822 6408 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 PAIRED WGS 19096316 SRR14894175 ftp.sra.ebi.ac.uk/vol1/fastq/SRR148/075/SRR14894175/SRR14894175_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR148/075/SRR14894175/SRR14894175_2.fastq.gz bede3671cd8d9e610734e053535e1325;0b6fa2b19cf6a12bdb2a01b4307044a3 1210582369;1226509211 Modi2021 2021 10.1016/j.quaint.2021.12.003 PsP_6407 SRA PRJNA739881 SRS9263817 6407 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 PAIRED WGS 19042125 SRR14894176 ftp.sra.ebi.ac.uk/vol1/fastq/SRR148/076/SRR14894176/SRR14894176_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR148/076/SRR14894176/SRR14894176_2.fastq.gz 774fbfff99c24bb7d339f86cb23edcb6;91529c496cd5623f36129b2f8a956d3d 1198906662;1200498099 Modi2021 2021 10.1016/j.quaint.2021.12.003 PsP_6405 SRA PRJNA739881 SRS9263816 6405 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 PAIRED WGS 19850768 SRR14894177 ftp.sra.ebi.ac.uk/vol1/fastq/SRR148/077/SRR14894177/SRR14894177_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR148/077/SRR14894177/SRR14894177_2.fastq.gz f6537d782e2b35ae9b1ee8fe34ea3320;13497615ba4031ba85160d53e709ae4f 1244765721;1246778274 +White2021 2021 10.3390/biology10121324 B2_B1 ENA PRJEB49091 ERS9769379 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212265 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212265/Ena.B.L021_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212265/Ena.L021_1.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B1 ENA PRJEB49091 ERS9769379 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212270 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212270/Ena.B.L021_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212270/Ena.L023_2.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B6 ENA PRJEB49091 ERS9769382 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212271 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212271/Ena.B.L024_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212271/Ena.L024_2.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B3 ENA PRJEB49091 ERS9769380 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212266 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212266/Ena.B.L024_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212266/Ena.L022_1.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B5 ENA PRJEB49091 ERS9769381 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212267 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212267/Ena.B.L025_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212267/Ena.L023_1.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B6 ENA PRJEB49091 ERS9769382 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212268 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212268/Ena.L021_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212268/Ena.L024_1.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B7 ENA PRJEB49091 ERS9769383 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212269 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212269/Ena.L022_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212269/Ena.L025_1.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B7 ENA PRJEB49091 ERS9769383 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212272 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212272/Ena.B.L025_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212272/Ena.L025_2.fastq.gz NA NA From 7af85cbfb25553330c273c0a425e2ec488fe4bdb Mon Sep 17 00:00:00 2001 From: DianaSpurite <112383244+DianaSpurite@users.noreply.github.com> Date: Mon, 19 Jun 2023 08:15:11 +0200 Subject: [PATCH 05/16] Update ancientsinglegenome-hostassociated_samples.tsv Added White 2021 samples --- ...ientsinglegenome-hostassociated_samples.tsv | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv index ad49ac91c..012347438 100644 --- a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv +++ b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv @@ -582,3 +582,21 @@ Eaton2023 2023 10.1016/j.cub.2023.01.064 Ole Wormsgade, Horsens Municipality 55. Eaton2023 2023 10.1016/j.cub.2023.01.064 Ole Wormsgade, Horsens Municipality 55.86 9.86 Denmark A1480 x1480 Homo sapiens 700 10.1016/j.cub.2023.01.064 bacteria Yersinia pestis tooth chromosome SRA raw PRJNA926136 SRS16579988 Rifkin2023 2023 10.1038/s42003-023-04582-y Ballito Bay -29.53 31.21 South Africa BBayA Homo sapiens 1900 10.1038/s42003-023-04582-y bacteria Rickettsia felis tissue chromosome SRA raw PRJNA930765 SRS16665771 Sarhan2023 2023 10.1186/s12915-022-01509-7 Barfüsserkirche/Franciscan church of Basel 47.554 7.589 Switzerland 3045 Homo sapiens 200 10.1186/s12915-022-01509-7 bacteria Mycolicibacterium sp. brain chromosome ENA raw PRJEB44723 ERS10216488 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769379 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B3 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769380 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B5 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769381 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B6 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769382 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B7 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769383 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769379 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769379 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B3 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769380 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B5 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769381 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B6 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769382 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B7 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769383 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769379 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769379 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B3 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769380 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B5 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769381 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B6 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769382 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B7 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769383 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769379 From 23d988b2fa7ed64e6227f98da3f54d6bcb6061f9 Mon Sep 17 00:00:00 2001 From: DianaSpurite <112383244+DianaSpurite@users.noreply.github.com> Date: Mon, 19 Jun 2023 08:19:53 +0200 Subject: [PATCH 06/16] Update ancientsinglegenome-hostassociated_libraries.tsv Adding White 2021 libraries. Certain entries missing (weren't in the ENA tables) --- .../ancientsinglegenome-hostassociated_libraries.tsv | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv index 35c48ebc5..febbc23dc 100644 --- a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv +++ b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv @@ -2277,3 +2277,11 @@ Eaton2023 2023 10.1016/j.cub.2023.01.064 A19 x21 SRA PRJNA926136 SRS16579972 D24 Eaton2023 2023 10.1016/j.cub.2023.01.064 A19 x21 SRA PRJNA926136 SRS16579972 D24a double AmpliTaq Gold DNA none Illumina HiSeq 2500 PAIRED WGS 933793 SRR23219989 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR232/089/SRR23219989/SRR23219989_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR232/089/SRR23219989/SRR23219989_2.fastq.gz 37108199f42f1296c3aacc9afb9ace7b;bfe803386227735b073e3376403fb4f5 49932402;58928402 Rifkin2023 2023 10.1038/s42003-023-04582-y BBayA SRA PRJNA930765 SRS16665771 baa001 single AccuPrime Pfx DNA none Illumina HiSeq 2500 SINGLE WGS 1225105 SRR23320768 fastq_mapped ftp.sra.ebi.ac.uk/vol1/fastq/SRR233/068/SRR23320768/SRR23320768.fastq.gz 0fd88effcdfcbdebff88b97308947bf8 15127737 Sarhan2023 2023 10.1186/s12915-022-01509-7 3045 ENA PRJEB44723 ERS10216488 3045 double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS 52823444 ERR8202909 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR820/009/ERR8202909/ERR8202909_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR820/009/ERR8202909/ERR8202909_2.fastq.gz 261a6f5fe988cffdf421303d7581b087;24bbe3ab0c9f460ef777936e3d5e676b 1775631371;2004262086 +White2021 2021 10.3390/biology10121324 B2_B1 ENA PRJEB49091 ERS9769379 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212265 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212265/Ena.B.L021_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212265/Ena.L021_1.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B1 ENA PRJEB49091 ERS9769379 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212270 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212270/Ena.B.L021_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212270/Ena.L023_2.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B6 ENA PRJEB49091 ERS9769382 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212271 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212271/Ena.B.L024_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212271/Ena.L024_2.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B3 ENA PRJEB49091 ERS9769380 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212266 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212266/Ena.B.L024_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212266/Ena.L022_1.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B5 ENA PRJEB49091 ERS9769381 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212267 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212267/Ena.B.L025_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212267/Ena.L023_1.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B6 ENA PRJEB49091 ERS9769382 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212268 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212268/Ena.L021_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212268/Ena.L024_1.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B7 ENA PRJEB49091 ERS9769383 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212269 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212269/Ena.L022_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212269/Ena.L025_1.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B7 ENA PRJEB49091 ERS9769383 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212272 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212272/Ena.B.L025_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212272/Ena.L025_2.fastq.gz NA NA From 78e5648f856811a7e8bb6260a80bce9110e16431 Mon Sep 17 00:00:00 2001 From: DianaSpurite <112383244+DianaSpurite@users.noreply.github.com> Date: Mon, 19 Jun 2023 08:22:37 +0200 Subject: [PATCH 07/16] Update ancientmetagenome-hostassociated_samples.tsv removed White 2021 samples from metagenome host associated --- ...ncientmetagenome-hostassociated_samples.tsv | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv b/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv index 31214ec9f..fc9ae5d5d 100644 --- a/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv +++ b/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv @@ -1398,21 +1398,3 @@ Honap2023 2023 10.1002/ajpa.24735 Sanders Site NA NA USA WAMP14 Homo sapiens 700 Honap2023 2023 10.1002/ajpa.24735 Horne 1 Site NA NA USA WAMP13 Homo sapiens 700 10.1002/ajpa.24735 oral dental calculus ENA PRJNA885571 SRS15300788 Honap2023 2023 10.1002/ajpa.24735 WRP 9 Site NA NA USA WAMP18 Homo sapiens 700 10.1002/ajpa.24735 oral dental calculus ENA PRJNA885571 SRS15300791 Honap2023 2023 10.1002/ajpa.24735 Selzer site NA NA USA WAMP34 Homo sapiens 700 10.1002/ajpa.24735 oral dental calculus ENA PRJNA885571 SRS15300804 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769379 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B3 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769380 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B5 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769381 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B6 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769382 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B7 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769383 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769379 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769379 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B3 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769380 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B5 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769381 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B6 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769382 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B7 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769383 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769379 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769379 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B3 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769380 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B5 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769381 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B6 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769382 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B7 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769383 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769379 From 8a6a53457e88e7326b59ed4fb6839d4dd55148f8 Mon Sep 17 00:00:00 2001 From: DianaSpurite <112383244+DianaSpurite@users.noreply.github.com> Date: Mon, 19 Jun 2023 08:24:17 +0200 Subject: [PATCH 08/16] Update ancientmetagenome-hostassociated_libraries.tsv Removing White 2021 libraries from the metagenome hostassociated --- .../ancientmetagenome-hostassociated_libraries.tsv | 9 --------- 1 file changed, 9 deletions(-) diff --git a/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv b/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv index 2ba92d9ee..f99917493 100644 --- a/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv +++ b/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv @@ -2374,12 +2374,3 @@ Honap2023 2023 10.1002/ajpa.24735 WAMP27 ENA PRJNA885571 SRS15300801 WAMP27B dou Honap2023 2023 10.1002/ajpa.24735 WAMP29 ENA PRJNA885571 SRS15300802 WAMP29 double AmpliTaq Gold DNA half-udg NA Illumina NovaSeq 6000 PAIRED WGS 50095058 SRR23699560 ftp.sra.ebi.ac.uk/vol1/fastq/SRR236/060/SRR23699560/SRR23699560_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR236/060/SRR23699560/SRR23699560_2.fastq.gz b205bdca8daa80da16785d6e8f553175;7d71a27d7699d0b3f790a128a9df196f 1435525598;1436696747 Honap2023 2023 10.1002/ajpa.24735 WAMP33 ENA PRJNA885571 SRS15300803 WAMP33 double AmpliTaq Gold DNA half-udg NA Illumina NovaSeq 6000 PAIRED WGS 33038410 SRR23699559 ftp.sra.ebi.ac.uk/vol1/fastq/SRR236/059/SRR23699559/SRR23699559_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR236/059/SRR23699559/SRR23699559_2.fastq.gz 1966b8a50f27bbdb40cb534433324ab5;a52dcd370f64dabe34a5df2415222172 874132258;876007254 Honap2023 2023 10.1002/ajpa.24735 WAMP34 ENA PRJNA885571 SRS15300804 WAMP34 double AmpliTaq Gold DNA half-udg NA Illumina NovaSeq 6000 PAIRED WGS 27167659 SRR23699558 ftp.sra.ebi.ac.uk/vol1/fastq/SRR236/058/SRR23699558/SRR23699558_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR236/058/SRR23699558/SRR23699558_2.fastq.gz 0de928f4e16c47256beea4b37ae62685;17de2f94a9fc13159702aba672c21fea 710293475;712747535 -White2021 2021 10.3390/biology10121324 B2_B1 ENA PRJEB49091 ERS9769379 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212265 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212265/Ena.B.L021_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212265/Ena.L021_1.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B1 ENA PRJEB49091 ERS9769379 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212270 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212270/Ena.B.L021_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212270/Ena.L023_2.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B6 ENA PRJEB49091 ERS9769382 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212271 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212271/Ena.B.L024_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212271/Ena.L024_2.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B3 ENA PRJEB49091 ERS9769380 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212266 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212266/Ena.B.L024_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212266/Ena.L022_1.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B5 ENA PRJEB49091 ERS9769381 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212267 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212267/Ena.B.L025_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212267/Ena.L023_1.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B6 ENA PRJEB49091 ERS9769382 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212268 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212268/Ena.L021_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212268/Ena.L024_1.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B7 ENA PRJEB49091 ERS9769383 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212269 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212269/Ena.L022_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212269/Ena.L025_1.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B7 ENA PRJEB49091 ERS9769383 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212272 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212272/Ena.B.L025_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212272/Ena.L025_2.fastq.gz NA NA - From 0965751af33f8501bb2f527645f706865bd8da75 Mon Sep 17 00:00:00 2001 From: DianaSpurite <112383244+DianaSpurite@users.noreply.github.com> Date: Mon, 19 Jun 2023 16:43:54 +0300 Subject: [PATCH 09/16] Update ancientsinglegenome-hostassociated_libraries.tsv --- ...ientsinglegenome-hostassociated_libraries.tsv | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv index febbc23dc..b8e078237 100644 --- a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv +++ b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv @@ -2277,11 +2277,11 @@ Eaton2023 2023 10.1016/j.cub.2023.01.064 A19 x21 SRA PRJNA926136 SRS16579972 D24 Eaton2023 2023 10.1016/j.cub.2023.01.064 A19 x21 SRA PRJNA926136 SRS16579972 D24a double AmpliTaq Gold DNA none Illumina HiSeq 2500 PAIRED WGS 933793 SRR23219989 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR232/089/SRR23219989/SRR23219989_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR232/089/SRR23219989/SRR23219989_2.fastq.gz 37108199f42f1296c3aacc9afb9ace7b;bfe803386227735b073e3376403fb4f5 49932402;58928402 Rifkin2023 2023 10.1038/s42003-023-04582-y BBayA SRA PRJNA930765 SRS16665771 baa001 single AccuPrime Pfx DNA none Illumina HiSeq 2500 SINGLE WGS 1225105 SRR23320768 fastq_mapped ftp.sra.ebi.ac.uk/vol1/fastq/SRR233/068/SRR23320768/SRR23320768.fastq.gz 0fd88effcdfcbdebff88b97308947bf8 15127737 Sarhan2023 2023 10.1186/s12915-022-01509-7 3045 ENA PRJEB44723 ERS10216488 3045 double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS 52823444 ERR8202909 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR820/009/ERR8202909/ERR8202909_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR820/009/ERR8202909/ERR8202909_2.fastq.gz 261a6f5fe988cffdf421303d7581b087;24bbe3ab0c9f460ef777936e3d5e676b 1775631371;2004262086 -White2021 2021 10.3390/biology10121324 B2_B1 ENA PRJEB49091 ERS9769379 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212265 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212265/Ena.B.L021_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212265/Ena.L021_1.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B1 ENA PRJEB49091 ERS9769379 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212270 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212270/Ena.B.L021_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212270/Ena.L023_2.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B6 ENA PRJEB49091 ERS9769382 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212271 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212271/Ena.B.L024_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212271/Ena.L024_2.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B3 ENA PRJEB49091 ERS9769380 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212266 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212266/Ena.B.L024_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212266/Ena.L022_1.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B5 ENA PRJEB49091 ERS9769381 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212267 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212267/Ena.B.L025_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212267/Ena.L023_1.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B6 ENA PRJEB49091 ERS9769382 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212268 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212268/Ena.L021_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212268/Ena.L024_1.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B7 ENA PRJEB49091 ERS9769383 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212269 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212269/Ena.L022_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212269/Ena.L025_1.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B7 ENA PRJEB49091 ERS9769383 unspecified double AmpliTaq Gold none Illumina HiSeq 4000 PAIRED WGS NA ERR11212272 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212272/Ena.B.L025_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212272/Ena.L025_2.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B1 ENA PRJEB49091 ERS9769379 unspecified double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS NA ERR11212265 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212265/Ena.B.L021_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212265/Ena.L021_1.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B1 ENA PRJEB49091 ERS9769379 unspecified double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS NA ERR11212270 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212270/Ena.B.L021_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212270/Ena.L023_2.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B6 ENA PRJEB49091 ERS9769382 unspecified double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS NA ERR11212271 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212271/Ena.B.L024_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212271/Ena.L024_2.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B3 ENA PRJEB49091 ERS9769380 unspecified double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS NA ERR11212266 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212266/Ena.B.L024_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212266/Ena.L022_1.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B5 ENA PRJEB49091 ERS9769381 unspecified double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS NA ERR11212267 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212267/Ena.B.L025_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212267/Ena.L023_1.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B6 ENA PRJEB49091 ERS9769382 unspecified double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS NA ERR11212268 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212268/Ena.L021_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212268/Ena.L024_1.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B7 ENA PRJEB49091 ERS9769383 unspecified double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS NA ERR11212269 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212269/Ena.L022_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212269/Ena.L025_1.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B7 ENA PRJEB49091 ERS9769383 unspecified double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS NA ERR11212272 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212272/Ena.B.L025_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212272/Ena.L025_2.fastq.gz NA NA From 9cb00b30ee43dd51abf25e1be5c5fd293abe3595 Mon Sep 17 00:00:00 2001 From: DianaSpurite <112383244+DianaSpurite@users.noreply.github.com> Date: Mon, 19 Jun 2023 16:57:06 +0300 Subject: [PATCH 10/16] Update ancientsinglegenome-hostassociated_samples.tsv --- .../samples/ancientsinglegenome-hostassociated_samples.tsv | 3 --- 1 file changed, 3 deletions(-) diff --git a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv index 012347438..656ec28eb 100644 --- a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv +++ b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv @@ -587,14 +587,11 @@ White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B3 White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B5 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769381 White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B6 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769382 White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B7 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769383 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769379 White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769379 White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B3 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769380 White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B5 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769381 White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B6 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769382 White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B7 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769383 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Treponema denticola tooth chromosome ENA raw PRJEB49091 ERS9769379 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769379 White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B3 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769380 White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B5 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769381 White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B6 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769382 From af136dad70be1d4bfbd4cd996c0f513cdde97d7e Mon Sep 17 00:00:00 2001 From: DianaSpurite <112383244+DianaSpurite@users.noreply.github.com> Date: Mon, 19 Jun 2023 17:09:07 +0300 Subject: [PATCH 11/16] Update CHANGELOG.md added white 2021 --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8776a2e06..fe838a23c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -44,6 +44,7 @@ and this project follows to [Calendar Versioning](https://calver.org/). - Eaton 2023 10.1016/j.cub.2023.01.064 (added by @DianaSpurite) - Rifkin 2023 10.1038/s42003-023-04582-y (added by @mibr30) - Sarhan 2023 10.1186/s12915-022-01509-7 (added by @msabrysarhan) +- White 2021 10.3390/biology10121324 (added by @DianaSpurite) #### Ancient Metagenome: Environmental @@ -80,7 +81,7 @@ and this project follows to [Calendar Versioning](https://calver.org/). - Vågene 2022 10.1038/s41467-022-28562-8 (added by @DianaSpurite) - Austin 2022 10.1038/s42003-022-03890-z (added by @DianaSpurite) - Guellil 2022 10.1126/sciadv.abo4435 (added by @DianaSpurite) -- Long 2022 10.1038/s42003-022-03527-1 (added by @jfy133 ) +- Long 2022 10.1038/s42003-022-03527-1 (added by @jfy133) #### Ancient Metagenome: Environmental From 1ee10609c78cf1b8ccc474d8c76516d9c9dd5e76 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alex=20H=C3=BCbner?= Date: Wed, 25 Sep 2024 11:25:53 +0200 Subject: [PATCH 12/16] Update library info after new upload of seq data to ENA --- ...ientsinglegenome-hostassociated_libraries.tsv | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv index 1ae13ef6c..5ae2a11e0 100644 --- a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv +++ b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv @@ -3105,11 +3105,11 @@ Lebrasseur2024 2024 10.1038/s41586-021-04018-9 UR17x29 ENA PRJEB44430 ERS7256200 Lebrasseur2024 2024 10.1038/s41586-021-04018-9 UR17x29 ENA PRJEB44430 ERS7256200 L1 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 SINGLE WGS 9413628 ERR6466108 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR646/008/ERR6466108/ERR6466108.fastq.gz 082fa661d3351c0fac22e2e922dc3795 342573885 Lebrasseur2024 2024 10.1038/s41586-021-04018-9 UR17x29 ENA PRJEB44430 ERS7256200 L2 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 SINGLE WGS 123717709 ERR6466109 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR646/009/ERR6466109/ERR6466109.fastq.gz 267fe0d4b684a1cf765ae560abdfbbc3 4352735230 Lebrasseur2024 2024 10.1038/s41586-021-04018-9 UR17x29 ENA PRJEB44430 ERS7256200 L4 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 SINGLE WGS 141415855 ERR6466111 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR646/001/ERR6466111/ERR6466111.fastq.gz 7bed95eb12f3d17c93fd6d47c5edfd04 4974034411 -White2021 2021 10.3390/biology10121324 B2_B1 ENA PRJEB49091 ERS9769379 unspecified double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS NA ERR11212265 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212265/Ena.B.L021_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212265/Ena.L021_1.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B1 ENA PRJEB49091 ERS9769379 unspecified double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS NA ERR11212270 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212270/Ena.B.L021_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212270/Ena.L023_2.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B6 ENA PRJEB49091 ERS9769382 unspecified double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS NA ERR11212271 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212271/Ena.B.L024_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212271/Ena.L024_2.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B3 ENA PRJEB49091 ERS9769380 unspecified double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS NA ERR11212266 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212266/Ena.B.L024_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212266/Ena.L022_1.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B5 ENA PRJEB49091 ERS9769381 unspecified double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS NA ERR11212267 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212267/Ena.B.L025_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212267/Ena.L023_1.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B6 ENA PRJEB49091 ERS9769382 unspecified double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS NA ERR11212268 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212268/Ena.L021_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212268/Ena.L024_1.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B7 ENA PRJEB49091 ERS9769383 unspecified double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS NA ERR11212269 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212269/Ena.L022_2.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212269/Ena.L025_1.fastq.gz NA NA -White2021 2021 10.3390/biology10121324 B2_B7 ENA PRJEB49091 ERS9769383 unspecified double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS NA ERR11212272 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212272/Ena.B.L025_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR11212272/Ena.L025_2.fastq.gz NA NA +White2021 2021 10.3390/biology10121324 B2_B1 ENA PRJEB49091 ERS9769379 L021 double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS 158433608 ERR13663672 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/072/ERR13663672/ERR13663672_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/072/ERR13663672/ERR13663672_2.fastq.gz 943cb5119373829c986bc95041da7f33;bc770e7de4cc196dab17a19e5115f210 3909717106;4206518326 +White2021 2021 10.3390/biology10121324 B2_B1 ENA PRJEB49091 ERS9769379 L021-B double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS 102400496 ERR13663671 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/071/ERR13663671/ERR13663671_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/071/ERR13663671/ERR13663671_2.fastq.gz 8e93e102502e20ceb06e8f02a53e589d;39a6078d490d1a476d42b0ed4177580b 2380509453;2570133344 +White2021 2021 10.3390/biology10121324 B2_B6 ENA PRJEB49091 ERS9769382 L024 double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS 164114498 ERR13663676 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/076/ERR13663676/ERR13663676_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/076/ERR13663676/ERR13663676_2.fastq.gz abafcc2b76f2d56f01e5c6ed95f0f20c;e65f30975fa8ff540a9083b77b25646b 4147933772;4482524602 +White2021 2021 10.3390/biology10121324 B2_B3 ENA PRJEB49091 ERS9769380 L022 double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS 172363072 ERR13663673 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/073/ERR13663673/ERR13663673_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/073/ERR13663673/ERR13663673_2.fastq.gz 93fe32a1e7baafdbe2ab5fde69a6d998;47cf6d5fec371200015a493a0839c828 4381516936;4643855551 +White2021 2021 10.3390/biology10121324 B2_B5 ENA PRJEB49091 ERS9769381 L023 double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS 165002236 ERR13663674 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/074/ERR13663674/ERR13663674_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/074/ERR13663674/ERR13663674_2.fastq.gz 370f2ee1d8d3929d4999d1ef6ba795f5;0390ac309d270d11f8ef01d1a98fe74f 4143803128;4491981331 +White2021 2021 10.3390/biology10121324 B2_B6 ENA PRJEB49091 ERS9769382 L024-B double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS 108865268 ERR13663675 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/075/ERR13663675/ERR13663675_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/075/ERR13663675/ERR13663675_2.fastq.gz 9f698e07345a859feb34cb4e99a55d11;d7d70554b02c6f5dc7952fd2485c163c 2589844121;2788114713 +White2021 2021 10.3390/biology10121324 B2_B7 ENA PRJEB49091 ERS9769383 L025-B double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS 81293780 ERR13663677 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/077/ERR13663677/ERR13663677_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/077/ERR13663677/ERR13663677_2.fastq.gz 00eb8d335bfedd6a0569e708bb5be5f8;3b34fc20b2c7a012ce5d25d177d55dc8 2074741912;2130629421 +White2021 2021 10.3390/biology10121324 B2_B7 ENA PRJEB49091 ERS9769383 L025 double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS 179780446 ERR13663678 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/078/ERR13663678/ERR13663678_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/078/ERR13663678/ERR13663678_2.fastq.gz 47149ec413c0a14645b7a838fc088507;1372803ee3d494b1876b82982c69d10c 4575913200;4879999751 From 7b3fe007b72d995dd15db9b262b4cd94337fb809 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alex=20H=C3=BCbner?= Date: Wed, 25 Sep 2024 11:28:04 +0200 Subject: [PATCH 13/16] Update CHANGELOG.md --- CHANGELOG.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5da511ead..3e93822f9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,8 @@ and this project follows to [Calendar Versioning](https://calver.org/). #### Ancient Single Genome: Host Associated +- White 2021 10.3390/biology10121324 (added by @DianaSpurite, @jfy133, and @alexhbnr) + #### Ancient Metagenome: Environmental ### Changed @@ -77,9 +79,6 @@ and this project follows to [Calendar Versioning](https://calver.org/). #### Ancient Single Genome: Host Associated -<<<<<<< HEAD -- White 2021 10.3390/biology10121324 -======= - Hodgkins 2023 10.1007/s13313-023-00936-6 (added by @DianaSpurite and @iseultj) >>>>>>> master From 541dce4727e8fa6bfca3d648b40ce4fffd489363 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 2 Oct 2024 10:53:32 +0200 Subject: [PATCH 14/16] Fix CHANGELOG --- CHANGELOG.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3e93822f9..1c3026e7b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -81,7 +81,6 @@ and this project follows to [Calendar Versioning](https://calver.org/). - Hodgkins 2023 10.1007/s13313-023-00936-6 (added by @DianaSpurite and @iseultj) ->>>>>>> master #### Ancient Metagenome: Environmental - Pérez 2023 10.1111/fwb.14182 (added by @ktozdogan) @@ -163,7 +162,6 @@ and this project follows to [Calendar Versioning](https://calver.org/). - Eaton 2023 10.1016/j.cub.2023.01.064 (added by @DianaSpurite) - Rifkin 2023 10.1038/s42003-023-04582-y (added by @mibr30) - Sarhan 2023 10.1186/s12915-022-01509-7 (added by @msabrysarhan) -- White 2021 10.3390/biology10121324 (added by @DianaSpurite) #### Ancient Metagenome: Environmental From 12d570d206dbbc1bc56fbb57af987b24d9130049 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 2 Oct 2024 11:10:25 +0200 Subject: [PATCH 15/16] Fix Lat:Lon precision and remove non-genome samples --- ...entsinglegenome-hostassociated_samples.tsv | 27 +++++++++---------- 1 file changed, 12 insertions(+), 15 deletions(-) diff --git a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv index 8478edaa0..bdadf8bb5 100644 --- a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv +++ b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv @@ -705,18 +705,15 @@ Sun2024 2024 10.1038/s41467-024-47358-6 QuanErGou 43.65 92.16 China XBQM46 Homo Sun2024 2024 10.1038/s41467-024-47358-6 QuanErGou 43.65 92.16 China XBQM125 Homo sapiens 2900 10.1038/s41467-024-47358-6 virus Hepatitis B virus bone chromosome GSA reference_aligned PRJCA020853 SAMC3135944 Sun2024 2024 10.1038/s41467-024-47358-6 BeiFang 37.13 81.61 China 11KBM13 Homo sapiens 3400 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135945 Lebrasseur2024 2024 10.1093/ve/vead087 Kamennyi Ambar 5 52.833 60.367 Russia UR17x29 Equus caballus 3800 10.1038/s41586-021-04018-9 virus Equid herpesvirus 4 bone chromosome ENA raw PRJEB44430 ERS7256200 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B1 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769379 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B3 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769380 -White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.72 Kazakhstan B2_B5 Homo sapiens 200 10.3390/biology10121324 bacteria Tannerella forsythia tooth chromosome ENA raw PRJEB49091 ERS9769381 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PRJEB49091 ERS9769383 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.720 Kazakhstan B2_B3 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769380 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.720 Kazakhstan B2_B5 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769381 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.720 Kazakhstan B2_B6 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769382 +White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.720 Kazakhstan B2_B7 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769383 From 4ea1d159cc6d078242af2be43e406edcbab767fe Mon Sep 17 00:00:00 2001 From: "James A. 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