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
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Additional credit

David F. Nieuwenhuijse, Alexey Sokolov


Views: 2591   Downloads: 225

Created: 12th Feb 2021 at 11:46

Last updated: 14th Nov 2023 at 10:59

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