Genomics - Read pre-processing without downloading from SRA
Version 1

Workflow Type: Galaxy

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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SEEK ID: https://workflowhub.eu/workflows/4?version=1

Inputs

ID	Name	Description	Type
0_Input Dataset Collection	n/a	n/a	File
1_Input Dataset Collection	n/a	n/a	File

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

Open master 302df99

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: 4775 Downloads: 790 Runs: 0

Created: 10th Apr 2020 at 13:06

Genomics - Read pre-processing without downloading from SRA Version 1