Workflow Type: Nextflow
Open
Deprecated
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 History
Version 1 (earliest) Created 12th Feb 2021 at 11:46 by Ross Thorne
Added/updated 1 files
Open
master
24e131f
Creators and Submitter
Creators
Not specifiedAdditional credit
David F. Nieuwenhuijse, Alexey Sokolov
Submitter
Activity
Views: 3199 Downloads: 307
Created: 12th Feb 2021 at 11:46
Last updated: 14th Nov 2023 at 10:59
Tags
This item has not yet been tagged.
Attributions
None
Collections