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

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Workflow Type: Galaxy

Removal of human reads from SARS-CoV-2 sequencing data

Associated Tutorial

This workflows is part of the tutorial GTN - Sequence Analyses - Removal of human reads from SARS-CoV-2 sequencing data, available in the GTN

Thanks to...

Tutorial Author(s): Wolfgang Maier

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1276?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

1.0 (latest) Created 16th Jul 2024 at 14:25 by Helena Rasche

Added/updated 4 files


Open master 299f010

2.0 (earliest) Created 25th Jun 2024 at 11:18 by Helena Rasche

Added/updated 4 files


Frozen 2.0 1175212
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
Trimmomatic
BWA
SAMtools
seqtk
License
Creative Commons Attribution 4.0 International
Activity

Views: 407   Downloads: 132

Created: 25th Jun 2024 at 11:18

Last updated: 25th Jun 2024 at 11:18

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Total size: 70.5 KB
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