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/

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
Total size: 51.3 KB
help Creators and Submitter
Creators
  • 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
License
Activity

Views: 882   Downloads: 40

Created: 10th Apr 2020 at 13:06

Last used: 27th Jan 2022 at 05:52

help Tags
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Version History

Version 1 (earliest) Created 10th Apr 2020 at 13:06 by Bert Droesbeke

Added/updated 3 files


Open master 302df99

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