Workflows
What is a Workflow?Filters
Query
Created At
Updated At
Workflow type
Nextflow2
Submitter
Ross Thorne2
Space
Independent Teams2
Maturity
Deprecated2
2
Workflows visible to you, out of a total of 2
Deprecated
A pipeline for mapping, calling, and annotation of SARS-CoV2 variants.
Deprecated
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 āNā.