ENA SARS-CoV-2 Nanopore Amplicon Sequencing Analysis Workflow Version 1
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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’.
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Created: 12th Feb 2021 at 11:46
Last used: 6th Mar 2021 at 23:40
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Version 1 Created 12th Feb 2021 at 11:46 by Ross Thorne
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Related items
Teams: SARS-CoV-2 Data Hubs
Organizations: EMBL-EBI
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
Teams: IBISBA Workflows, NMR Workflow, UNLOCK, NanoGalaxy, Galaxy Climate, PNDB, IMBforge, COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource, LBI-RUD, Nick-test-team, usegalaxy-eu, Italy-Covid-data-Portal, UX trial team, Integrated and Urban Plant Pathology Laboratory, SARS-CoV-2 Data Hubs, lmjxteam2, Australian BioCommons, virAnnot pipeline
Web page: Not specified
The SARS-CoV-2 Data Hubs form one of the three components of the European COVID-19 Data Platform. Using technology that builds upon existing EMBL-EBI infrastructure, we provide SARS-CoV-2 Data Hubs to those public health agencies and other scientific groups responsible for generating viral sequence data from the outbreak at national or regional levels. SARS-CoV-2 Data Hubs offer a variety of configurations in terms of upload tools, data processing and analysis workflows and data visualisations.
Space: Independent Teams
Public web page: https://www.covid19dataportal.org/
