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