README.md

MiAW

MiSeq Analysis Workflow of CDC central lab

Installation

conda env create -f requirement.yaml

Pipeline

Usage

Basic

python miaw.py -1 <R1.fastq> -2 <R2.fastq> -o <output_dir>

Classify with Kraken2

python miaw.py -1 <R1.fastq> -2 <R2.fastq> -o <output_dir> --kraken2_db <database>

• Can find pre-build database in here

Check genome completeness with BUSCO

python miaw.py -1 <R1.fastq> -2 <R2.fastq> -o <output_dir> --busco_db <database>