Workflow Type: Nextflow
A workflow for mapping and consensus generation of SARS-CoV2 whole genome amplicon nanopore data implemented in the Nextflow framework. Reads are mapped to a reference genome using Minimap2 after trimming the amplicon primers with a fixed length at both ends of the amplicons using Cutadapt. The consensus is called using Pysam based on a majority read support threshold per position of the Minimap2 alignment and positions with less than 30x coverage are masked using ‘N’.
Version 1 (earliest) Created 12th Feb 2021 at 11:46 by Ross Thorne
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Views: 1480 Downloads: 47
Created: 12th Feb 2021 at 11:46
Total size: 2.76 KB