NCBI SARS-CoV-2 Variant Calling (SC2VC) Pipeline

Contact:

email: [email protected]

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The NCBI SARS-CoV-2 Variant Calling (SC2VC) Pipeline is a collection of snakemake workflows that allows calling high-confidence variants from SARS-CoV-2 NGS data in a standardized format. An overview for the pipeline is available here.

Results are available via following NCBI resources: NCBI SARS-COV-2 at AWS, NCBI SARS-COV-2 at GCP

Also, available as: Weekly ACTIV-TRACE reports

Content:

• Wrapper script to run workflow:
  • run.sh
• Reference sequence and snpEff databases:
  • toolbox/static/reference/
  • toolbox/static/snpEff/

Dependencies:

Following third party tools assumed to be installed in user environment:

• samtools:
  • htslib
  • samtools
  • bcftools
• mummer
• snpEff
• trimmomatic
• minimap2
• SRA-toolkit
• Picard
• GATK
• medaka
• hisat2
• vcftools

For the comprehensive list of tools used and their versions, please refer to Dockerfile

Reference sequence indexing

Pipeline expect reference sequence to be indexed, to create these indexes please run

gatk CreateSequenceDictionary -R toolbox/static/reference/NC_045512.2.fa
samtools faidx toolbox/static/reference/NC_045512.2.fa
gatk IndexFeatureFile --input toolbox/static/reference/NC_045512.2.known_sites.vcf
hisat2-build toolbox/static/reference/NC_045512.2.fa toolbox/static/reference/NC_045512.2.fa

Usage:

  run.sh --platform --accession|--list [--instrument] [--conf] [--workdir] [--help]
    --platform:   platform, choices = [illumina, ont, pacbio, genbank], default = illumina
    --instrument: applicable to ONT platform only, use with single accession option, default = PromethION
    --accession:  single accession, optional, either --accession or --list must be specified
    --list:       file with accession list, optional, either --accession or --list must be specified
                  NOTE: ONT file list is expected to have at least two columns: <acc> <instrument>
    --conf:       optional custom configfile to override default
    --workdir:    optional working directory, default = ./workdir
    --help:       to display this help

Usage examples:

1. ILLUMINA

   toolbox/workflow/run.sh --accession SRR21830388
   # in case of using docker image
   /pipelines/toolbox/workflow/run.sh --accession SRR21830388 --conf /pipelines/toolbox/workflow/extra.config.yaml 

2. OXFORD-NANOPORE

   toolbox/workflow/run.sh --accession SRR15965069 --platform ont --instrument GridION

3. PacBio

   toolbox/workflow/run.sh --accession SRR14895419 --platform pacbio