mgi-ncov19-snakemake

This snakemake pipeline can conduct cov-19 virus classification, de novo assembly, coverage assessment and variant calling.

The pipeline is built according to https://github.com/BGI-IORI/nCoV_Meta (preprint: https://doi.org/10.1101/2020.03.16.993584)

Differences between mgi-ncov19-snakemake and nCoV_Meta:

1. low complexity reads removal were implemented with fastp (bgi: prinSEQ)
2. kraken2 was employed in this snakemake pipeline (bgi: kraken1)
3. SOAPnuke v2 (bgi: SOAPnuke v1) (better to change to SOAPnuke v1)
4. not yet finished with the alignment and variant calling steps.

updated: 2020-04-14

Usage:

0. Install Conda and Snakemake

1. Clone workflow

git clone [email protected]:huyue87/mgi-ncov19-snakemake

2. Execute workflow

# 2.1 load input files (paired-end raw reads)
cd mgi-ncov19-snakemake/input
ln -s Sample_{1,2}.fq.gz . 

# 2.2 run de novo assembly and generating sam files
cd mgi-ncov19-snakemake
snakemake --use-conda -n 
snakemake --use-conda