covdrop

Pipeline for detecting primer dropout in SARS-CoV-2 tiled amplicon genomes.

Install

Github

git clone https://github.com/MDU-PHL/covdrop.git && cd covdrop

snakemake --use-conda -j -C fasta=samples.fa bed=artic_v4.1.bed reference=wuhCor1.fa

SNK

snk install MDU-PHL/covdrop -s 7.32.4

covdrop run --fasta samples.fa --bed artic_v4.1.bed

Heatmap