Genomics - Read pre-processing
Version 1

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Workflow Type: Galaxy

Preprocessing of raw SARS-CoV-2 reads. More info can be found at https://covid19.galaxyproject.org/genomics/

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SEEK ID: https://workflowhub.eu/workflows/2?version=1

Inputs

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

Steps

ID	Name	Description
10_MultiQC	n/a	n/a
11_Filter SAM or BAM, output SAM or BAM	n/a	n/a
12_Filter SAM or BAM, output SAM or BAM	n/a	n/a
13_MergeSamFiles	n/a	n/a
14_MergeSamFiles	n/a	n/a
15_Samtools fastx	n/a	n/a
16_Samtools fastx	n/a	n/a
2_Faster Download and Extract Reads in FASTQ	n/a	n/a
3_Faster Download and Extract Reads in FASTQ	n/a	n/a
4_fastp	n/a	n/a
5_NanoPlot	n/a	n/a
6_FastQC	n/a	n/a
7_Map with minimap2	n/a	n/a
8_MultiQC	n/a	n/a
9_Map with BWA-MEM	n/a	n/a

Version History

Version 1 (earliest) Created 10th Apr 2020 at 11:20 by Bert Droesbeke

Added/updated 3 files

Open master 571baa6

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: 4879 Downloads: 810 Runs: 3

Created: 10th Apr 2020 at 11:20

Genomics - Read pre-processing Version 1