Workflow Type: Galaxy
Stable

The workflow takes a HiFi reads collection, runs FastQC and SeqKit, filters with Cutadapt, and creates a MultiQC report. The main outputs are a collection of filtred reads, a report with raw and filtered reads stats, and a table with raw reads stats.

Inputs

ID Name Description Type
HiFi raw reads collection #main/HiFi raw reads collection n/a
  • array containing
    • File

Steps

ID Name Description
1 FastQC HiFi raw toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
2 SeqKit HiFi raw toolshed.g2.bx.psu.edu/repos/iuc/seqkit_stats/seqkit_stats/2.10.0+galaxy0
3 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0
4 SeqKit HiFi toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
5 MultiQC HiFi toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3

Outputs

ID Name Description Type
HiFi trimmed collection #main/HiFi trimmed collection n/a
  • File
SeqKit HiFi raw table #main/SeqKit HiFi raw table n/a
  • File
html_report #main/html_report n/a
  • File

Version History

Version 2 (latest) Created 18th Sep 2024 at 14:14 by Diego De Panis

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Open master 62f2b97

Version 1 (earliest) Created 6th Oct 2023 at 14:17 by Diego De Panis

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Frozen Version-1 558378a
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Views: 5634   Downloads: 597   Runs: 69

Created: 6th Oct 2023 at 14:17

Last updated: 1st Jun 2025 at 13:03

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