From ab0baca010d7cc2f92aa8d031ca38c3eeb012867 Mon Sep 17 00:00:00 2001 From: Jon Palmer Date: Sat, 3 Oct 2015 17:19:32 -0500 Subject: [PATCH] bug fixes, update v0.1.1 --- README.md | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 6819350..ee17fd3 100644 --- a/README.md +++ b/README.md @@ -17,19 +17,23 @@ UFITS comes with a wrapper script for ease of use. On UNIX, you can call it by ``` $ ufits.py Usage: ufits -version: 0.1.0 +version: 0.1.1 Command: ion pre-process Ion Torrent data (find barcodes, trim/pad) illumina pre-process folder of de-multiplexed Illumina data (gunzip, merge PE, trim/pad, concatenate) cluster cluster OTUs (using UPARSE algorithm) filter OTU table filtering + heatmap Create heatmap from OTU table + +Written by Jon Palmer (2015) nextgenusfs@gmail.com + ``` And then by calling one of the commands, you get a help menu for each: ``` -$ ufits cluster +$ ufits.py cluster Usage: ufits cluster -version: 0.1.0 +version: 0.1.1 Arguments: -i, --fastq Input FASTQ file (Required) -o, --out Output base name. Default: out @@ -39,11 +43,14 @@ Arguments: -i, --fastq Input FASTQ file (Required) -l, --length Length to trim reads. Default 250 --mock Name of spike-in mock community. Default: None --mc Mock community FASTA file. Default: ufits_mock3.fa - --uchime_ref Run Chimera filtering. Default: off (ITS1, ITS2, Full) + --uchime_ref Run Chimera filtering. Default: off [ITS1, ITS2, Full] --map_unfiltered Map unfiltered reads back to OTUs. Default: off - --unoise Run De-noising pre-clustering UNOISE. Default: off + --unoise Run De-noising pre-clustering (UNOISE). Default: off --size_annotations Append size annotations to OTU names. Default: off -u, --usearch USEARCH executable. Default: usearch8 + +Written by Jon Palmer (2015) nextgenusfs@gmail.com + ``` ####Processing Ion Torrent Data:#### @@ -100,5 +107,4 @@ Coming soon.... UTAX, RDP, BLAST ####Dependencies#### -python, biopython, USEARCH8 (accessible in PATH; alternatively you can pass in the variable `-u /path/to/usearch8` to scripts requiring USEARCH8). - +python, biopython, USEARCH8 (accessible in PATH; alternatively you can pass in the variable `-u /path/to/usearch8` to scripts requiring USEARCH8). In order to draw a heatmap using `ufits.py heatmap` you will need to have the following python libraries installed: `matplotlib, pandas, numpy`. They can be installed with pip, i.e. `pip install matplotlib pandas numpy`. \ No newline at end of file