COVID-19 variant calling pipeline

This repository contains workflows for processing SARS-CoV-2 data.

The FASTQ-based workflows produce variant calls, assembled genomes, and lineage assignments from raw sequencing reads. The FASTQ-based workflows are able to process reads originating from PacBio, Oxford Nanopore (single-end), and Illumina (paired-end) sequencing data.

An assembly-based workflow which calculates pseudo-variant sites and as

This is a companion discussion topic for the original entry at