A pipline to detect variant in sequencing data of SARS-CoV-2

Installation

Bioconda is required to install the tool

Use the following command to install and activate the environment

conda env update --file https://raw.githubusercontent.com/wuaipinglab/sra2variant/main/environment.yml
conda activate sra2variant

If the above doesn't work because of the network issue, try

conda env update --file https://raw.githubusercontent.com/wuaipinglab/sra2variant/main/environment2.yml
conda activate sra2variant

Quickstart

WGS PE

1. First a reference genome in fasta format is needed. The following command downloads and store the genome as reference/NC_045512.2.fasta.

mkdir ./reference
wget https://raw.githubusercontent.com/wuaipinglab/sra2variant/main/sra2variant/data/NC_045512.2.fasta
mv NC_045512.2.fasta ./reference

2. Download reads files in sra format and store them in a separate directory. Here two sra files are stored in ./wgs_reads directory.

mkdir ./wgs_reads
prefetch -o ./wgs_reads/SRR14119630.sra SRR14119630
prefetch -o ./wgs_reads/SRR14119629.sra SRR14119629

3. Use the pipeline for WGS paired end reads. In this example, We use the reference genome ./reference/NC_045512.2.fasta to analyze all sra files in ./wgs_reads directory.

sra2variant-WGS-PE -r ./reference/NC_045512.2.fasta -i ./wgs_reads

ARTIC PE

1. First a reference genome in fasta format, artic primer in bed format and a amplicon assignment in tsv format are needed. The following command downloads and store the files in reference.

mkdir ./reference

wget https://raw.githubusercontent.com/wuaipinglab/sra2variant/main/sra2variant/data/NC_045512.2.fasta
mv NC_045512.2.fasta ./reference

wget https://raw.githubusercontent.com/wuaipinglab/sra2variant/main/sra2variant/data/ARTIC_nCoV-2019_v3.bed
mv ARTIC_nCoV-2019_v3.bed ./reference

wget https://raw.githubusercontent.com/wuaipinglab/sra2variant/main/sra2variant/data/ARTIC_amplicon_info_v3.tsv
mv ARTIC_amplicon_info_v3.tsv ./reference

2. Download reads files in sra format and store them in a separate directory. Here two sra files are stored in ./artic_reads directory.

mkdir ./artic_reads
prefetch -o ./artic_reads/SRR14388832.sra SRR14388832
prefetch -o ./artic_reads/SRR14398873.sra SRR14398873

3. Use the pipeline for WGS paired end reads. In this example, We use the reference genome ./reference/NC_045512.2.fasta to analyze all sra files in ./artic_reads directory.

sra2variant-ARTIC-PE -r ./reference/NC_045512.2.fasta \
                     -p ./reference/ARTIC_nCoV-2019_v3.bed \
                     -a ./reference/ARTIC_amplicon_info_v3.tsv \
                     -i ./artic_reads/

Other pipelines are under development