Genomics - PE Variation
Version 1

Workflow Type: Galaxy

Analysis of variation within individual COVID-19 samples using Illumina Paired End data. More info can be found at https://covid19.galaxyproject.org/genomics/

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SEEK ID: https://workflowhub.eu/workflows/7?version=1

Inputs

ID	Name	Description	Type
GenBank file	n/a	n/a	File
Paired Collection (fastqsanger)	n/a	n/a	File

Steps

ID	Name	Description
10_Realign reads	n/a	n/a
11_MultiQC	n/a	n/a
12_Call variants	n/a	n/a
13_SnpEff eff	n/a	n/a
14_SnpSift Extract Fields	n/a	n/a
15_Collapse Collection	n/a	n/a
2_SnpEff build	n/a	n/a
3_fastp	n/a	n/a
4_Map with BWA-MEM	n/a	n/a
5_MultiQC	n/a	n/a
6_Filter SAM or BAM, output SAM or BAM	n/a	n/a
7_Samtools stats	n/a	n/a
8_MarkDuplicates	n/a	n/a
9_MultiQC	n/a	n/a

Version History

Version 1 (earliest) Created 10th Apr 2020 at 13:52 by Bert Droesbeke

Added/updated 3 files

Open master 1f96884

Creators and Submitter

Creators

Not specified

Additional credit

Dannon Baker, Marius van den Beek, Dave Bouvier, John Chilton, Nate Coraor, Frederik Coppens, Bert Droesbeke, Ignacio Eguinoa, Simon Gladman, Björn Grüning, Delphine Larivière, Gildas Le Corguillé, Andrew Lonie, Nicholas Keener, Sergei Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver

Submitter

Bert Droesbeke

License

MIT License

Activity

Views: 2714 Downloads: 321

Created: 10th Apr 2020 at 13:52

Genomics - PE Variation Version 1