ENA SARS-CoV-2 Nanopore Amplicon Sequencing Analysis Workflow
Version 1

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 History

Version 1 (earliest) Created 12th Feb 2021 at 11:46 by Ross Thorne

Added/updated 1 files

Open master 24e131f
help Creators and Submitter
Not specified
Additional credit

David F. Nieuwenhuijse, Alexey Sokolov


Views: 968   Downloads: 40

Created: 12th Feb 2021 at 11:46

Last used: 29th Sep 2022 at 23:28

help Attributions


Total size: 2.76 KB
Powered by
Copyright © 2008 - 2022 The University of Manchester and HITS gGmbH

By continuing to use this site you agree to the use of cookies