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

Workflow Type: Nextflow
Work-in-progress

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 ā€˜Nā€™.

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
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Additional credit

David F. Nieuwenhuijse, Alexey Sokolov

Submitter
Activity

Views: 806   Downloads: 39

Created: 12th Feb 2021 at 11:46

Last used: 24th Jun 2022 at 07:28

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Total size: 2.76 KB
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