GTN - Sequence Analyses - Removal of human reads from SARS-CoV-2 sequencing data
Version 1

Visit source Download RO Crate
Workflow Type: Galaxy

Galaxy workflow

SEEK ID: https://dev.workflowhub.eu/workflows/899?version=1

Inputs

ID Name Description Type
Input Dataset Collection #main/Input Dataset Collection n/a
  • array containing
    • File

Steps

ID Name Description
1 Trimmomatic toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1
2 Unzip Collection __UNZIP_COLLECTION__
3 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2
4 Samtools fastx toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1
5 Select Grep1
6 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2
7 seqtk_subseq toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1
8 seqtk_subseq toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1
9 Paired-end collection of cleaned reads __ZIP_COLLECTION__

Outputs

ID Name Description Type
Cleaned Data #main/Cleaned Data n/a
  • File
_anonymous_output_10 #main/_anonymous_output_10 n/a
  • File
_anonymous_output_11 #main/_anonymous_output_11 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
_anonymous_output_3 #main/_anonymous_output_3 n/a
  • File
_anonymous_output_4 #main/_anonymous_output_4 n/a
  • File
_anonymous_output_5 #main/_anonymous_output_5 n/a
  • File
_anonymous_output_6 #main/_anonymous_output_6 n/a
  • File
_anonymous_output_7 #main/_anonymous_output_7 n/a
  • File
_anonymous_output_8 #main/_anonymous_output_8 n/a
  • File
_anonymous_output_9 #main/_anonymous_output_9 n/a
  • File

Version History

2 (earliest) Created 22nd Apr 2024 at 11:02 by Helena Rasche

Added/updated 3 files


Open master a72be73
help Creators and Submitter
Creators
Not specified
Submitter
Tools
Trimmomatic
BWA
SAMtools
seqtk
License
Creative Commons Attribution 4.0 International
Activity

Views: 31

Created: 22nd Apr 2024 at 11:02

Last updated: 22nd Apr 2024 at 11:02

help Attributions

None

Total size: 24.3 KB
Powered by
 (v.1.15.0-pre)
About Dev WorkflowHub | Acknowledgements | Credits | Terms & Conditions | Privacy Policy
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH