Workflows

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A version of V-pipe (analysis of next generation sequencing (NGS) data from viral pathogens) specifically adapted to analyze high-throughput sequencing data of SARS-CoV-2.

Alignment, assembly and annotation of RNQSEQ reads using TOPHAT (without filtering out host reads).

Alignment, assembly RNASEQ reads and annotation of generated transcripts.

Alignment, assembly and annotation of RNASEQ reads as well as annotation of generated transcripts.

Alignment, assembly and annotation of generated transcripts from RNASEQ reads.

Virus genome assembly with Unicycler and Spades, The 2 assemblers works in parallel. The graph visualization is made with Bandage. workflow git repository : https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/blob/master/Assembly/workflow/assembly-wf-virus.cwl Based on https://github.com/galaxyproject/SARS-CoV-2/blob/master/genomics/2-Assembly/as_wf.png

Analysis of variation within individual COVID-19 samples using bowtie2, bwa, fastp, multiqc , picard ,samtools, snpEff Workflow, tools and data are available on https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/tree/master/Variation This worklow was ported into CWL from a Galaxy Workflow ( https://github.com/galaxyproject/SARS-CoV-2/tree/master/genomics/4-Variation migrated to CWL).

Author: AMBARISH KUMAR er.ambarish@gmail.com; ambari73_sit@jnu.ac.in

This is a proposed standard operating procedure for genomic variant detection using SAMTools.

It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.

It uses Illumina RNASEQ reads and genome sequence.

Detects SNPs and INDELs using VARSCAN2.