Workflows

What is a Workflow?
2 Workflows visible to you, out of a total of 2
Deprecated

A pipeline for mapping, calling, and annotation of SARS-CoV2 variants.

Type: Nextflow

Creator: Krisztian Papp

Submitter: Ross Thorne

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 ā€˜Nā€™.

Type: Nextflow

Creator: David F. Nieuwenhuijse, Alexey Sokolov

Submitter: Ross Thorne

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