nf-ninjaIndex - Create an ninjaIndex for nf-ninjaMap

Procedure for building an ninja index directory for ninjaMap

0. Copy all genomes into a folder, e.g., genomes/, then the following script to create the required index files

python scripts/create_ninjamap_db.py -list HCom2.seedfile.csv -db HCom2

The seedfile format

Note that the seedfile is a CSV (comma-separated values) file with its header

The format of the seedfile is Strain_Name,FTP_link

Strain_Name,FTP_link
Acidaminococcus-fermentans-DSM-20731-MAF-2,/path/to/HCom2_20221117/genomes/Acidaminococcus-fermentans-DSM-20731-MAF-2.fna
Acidaminococcus-sp-D21-MAF-2,path/to/HCom2_20221117/genomes/Acidaminococcus-sp-D21-MAF-2.fna
........

After running the above script successfully, you should see two folders, fasta and db. The former contains all the reformated strains, and the latter contains all the db related files.

1. Build a binmap file in the db folder and rename it depending on your project, e.g., HCom2.ninjaIndex.binmap.csv Please see the job submission examples in building ninjaIndex

2. Create a bowtie2 index (prefix: HCom2) directory using the concatenated genome file (HCom2.fna)

docker container run --rm \
    --workdir $(pwd) \
    --volume $(pwd):$(pwd) \
    quay.io/biocontainers/bowtie2:2.4.1--py38he513fc3_0 \
        bowtie2-build \
        --threads 8 \
        --seed 1712 \
        -f HCom2.fna HCom2 && mkdir -p bowtie2_index

mkdir -p bowtie2_index
mv *bt2 bowtie2_index

3. Copy the Binmap file and bowtie2 index files to the database folder

Index directory structure

Database folder: HCom2_20221117 Database prefix: HCom2 Binmap file: HCom2.ninjaIndex.binmap.csv

HCom2_20221117/
├── db
│   ├── HCom2.db_metadata.tsv (not required)
│   ├── HCom2.fna (concatenated genome file)
│   ├── HCom2.ninjaIndex.binmap.csv (ninja index)
│   ├── HCom2.nm_mates_bin.tsv  (not required)
│   ├── HCom2.per_genome_metadata.tsv  (not required)
│   └── bowtie2_index  ( bowtie2 index of the concatenated genome file)
│       ├── HCom2.1.bt2
│       ├── HCom2.2.bt2
│       ├── HCom2.3.bt2
│       ├── HCom2.4.bt2
│       ├── HCom2.rev.1.bt2
│       └── HCom2.rev.2.bt2
└── fasta
    ├── Acidaminococcus-fermentans-DSM-20731-MAF-2.fna
    ├── Acidaminococcus-sp-D21-MAF-2.fna
    ├── Adlercreutzia-equolifaciens-DSM-19450.fna
    ├── Akkermansia-muciniphila-ATCC-BAA-835-MAF-2.fna
        ...............................................

An example of ninjaMap Index (hCom2) is available at

https://zenodo.org/record/7872423/files/hCom2_20221117.ninjaIndex.tar.gz

Nextflow Introduction

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.