read-pipeline

Short read pipeline of CIWARS for taxonomy classification of bacterial pathogens and computation of ARG abundance based on rpoB marker gene normalization

Requirements

1. Linux operating system
2. conda

Installation

git clone https://github.com/muhit-emon/read-pipeline.git
cd read-pipeline
bash install.sh
conda env create -f environment.yml

conda environment activation

After installation, a conda environment named read_pipeline will be created.
To activate the environment, run the following command

conda activate read_pipeline

Download bacterial pathogen database (22 GB) and non-prokaryote database (11 GB)

Go inside read-pipeline directory. Download the pathogen DB and non-prokaryote DB compatible with Kraken2 and uncompress them.

wget https://zenodo.org/records/14537567/files/CIWARS_Pathogen_DB.tar.gz
tar -zxvf CIWARS_Pathogen_DB.tar.gz
rm CIWARS_Pathogen_DB.tar.gz

wget https://zenodo.org/records/14537567/files/non-prokaryote-DB.tar.gz
tar -zxvf non-prokaryote-DB.tar.gz
rm non-prokaryote-DB.tar.gz

Usage on metagenomic paired-end short read data

Go inside read-pipeline directory.

To run the short read pipeline on metagenomic paired-end short read data ( * .fastq/ * .fq/ * .fastq.gz/ * .fq.gz), use the following command

nextflow run short-read-pipeline.nf --R1 <absolute/path/to/forward/read/file> --R2 <absolute/path/to/reverse/read/file> --out_fname <prefix of output file name>
rm -r work

The command line options for this script (short-read-pipeline.nf) are:

--R1: The absolute path of the fastq file containing forward read sequences
--R2: The absolute path of the fastq file containing reverse read sequences
--out_fname: The prefix of the output file name

With --out_fname S1, output files named S1.k2report, S1_rpoB_ARG_norm.tsv, and S1_drug_wise_rpoB_norm.tsv will be generated inside read-pipeline directory.