Genomics - Read pre-processing
Version 1

Workflow Type: Galaxy

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

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
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Creators
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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
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Activity

Views: 1384   Downloads: 47

Created: 10th Apr 2020 at 11:20

Last used: 27th Jun 2022 at 03:56

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Total size: 60.3 KB
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