Workflow Type: Galaxy
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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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Inputs
ID | Name | Description | Type |
---|---|---|---|
GenBank file | n/a | n/a |
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Paired Collection (fastqsanger) | n/a | n/a |
|
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
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Creators and Submitter
Creators
Not specifiedAdditional 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
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Created: 10th Apr 2020 at 13:52
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