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


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€™.

help Creators and Submitter
  • David F. Nieuwenhuijse
  • Alexey Sokolov

Views: 168   Downloads: 13

Created: 12th Feb 2021 at 11:46

Last used: 11th May 2021 at 03:55

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Version History

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

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