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72 Workflows visible to you, out of a total of 72
COVID-19-PE-WGS-ILLUMINA (v0.1)

COVID-19: variation analysis on WGS PE data

This workflows performs paired end read mapping with bwa-mem followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff 4.5covid19.

Type: Galaxy

Creator: Wolfgang Maier

Submitter: WorkflowHub Sandbox Bot

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COVID-19-PE-ARTIC-ILLUMINA (v0.1)

COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ARTIC data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming ARTIC primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by ARTIC primer-binding site mutations and excludes reads derived from such "tainted" amplicons ...

Type: Galaxy

Creator: Wolfgang Maier

Submitter: WorkflowHub Sandbox Bot

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