This repository contains two pipelines for processing SARS-CoV-2 data:
- The “from assembly” pipeline converts assembled SARS-CoV-2 genomes to variant calls.
- 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.
This is a companion discussion topic for the original entry at github.com/DNAstack/covid-processing-pipeline/covid-19-varcal-from-assembly