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

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
#main/0_Input Dataset Collection n/a n/a File
#main/1_Input Dataset Collection n/a n/a File

Steps

ID Name Description
#main/10_Filter SAM or BAM, output SAM or BAM
#main/11_MergeSamFiles
#main/12_MergeSamFiles
#main/13_Samtools fastx
#main/14_Samtools fastx
#main/2_fastp
#main/3_NanoPlot
#main/4_FastQC
#main/5_Map with minimap2
#main/6_MultiQC
#main/7_Map with BWA-MEM
#main/8_MultiQC
#main/9_Filter SAM or BAM, output SAM or BAM
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: 555   Downloads: 29

Created: 10th Apr 2020 at 13:06

Last used: 11th May 2021 at 04:13

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Version History

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

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