Workflow Type: Galaxy
Open
Preprocessing of raw SARS-CoV-2 reads. This workflow contains an alternate starting point to avoid the data to be downloaded from the NCBI SRA. More info can be found at https://covid19.galaxyproject.org/genomics/
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Inputs
ID | Name | Description | Type |
---|---|---|---|
0_Input Dataset Collection | n/a | n/a |
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1_Input Dataset Collection | n/a | n/a |
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Steps
ID | Name | Description |
---|---|---|
10_Filter SAM or BAM, output SAM or BAM | n/a | n/a |
11_MergeSamFiles | n/a | n/a |
12_MergeSamFiles | n/a | n/a |
13_Samtools fastx | n/a | n/a |
14_Samtools fastx | n/a | n/a |
2_fastp | n/a | n/a |
3_NanoPlot | n/a | n/a |
4_FastQC | n/a | n/a |
5_Map with minimap2 | n/a | n/a |
6_MultiQC | n/a | n/a |
7_Map with BWA-MEM | n/a | n/a |
8_MultiQC | n/a | n/a |
9_Filter SAM or BAM, output SAM or BAM | n/a | n/a |
Version History
Version 1 (earliest) Created 10th Apr 2020 at 13:06 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
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Created: 10th Apr 2020 at 13:06
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