github.com/DNAstack/covid-processing-pipeline/covid-19-varcal-from-assembly

Automatic Tools and Workflows
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COVID-19 variant calling pipeline

This repository contains two pipelines for processing SARS-CoV-2 data:

  1. The “from assembly” pipeline converts assembled SARS-CoV-2 genomes to variant calls.
  2. The “from fastq” pipeline converts from raw reads (fastqs) to variants and assembly files. This pipeline is able to process both Nanopore (single-end) and Illumina paired-end sequencing data.

Required software

This is a companion discussion topic for the original entry at github.com/DNAstack/covid-processing-pipeline/covid-19-varcal-from-assembly