Workflow Type: Galaxy

Data QC step, can run alone or as part of a combined workflow for large genome assembly.

  • What it does: Reports statistics from sequencing reads.
  • Inputs: long reads (fastq.gz format), short reads (R1 and R2) (fastq.gz format).
  • Outputs: For long reads: a nanoplot report (the HTML report summarizes all the information). For short reads: a MultiQC report.
  • Tools used: Nanoplot, FastQC, MultiQC.
  • Input parameters: None required.
  • Workflow steps: Long reads are analysed by Nanoplot; Short reads (R1 and R2) are analysed by FastQC; the resulting reports are processed by MultiQC.
  • Options: see the tool settings options at runtime and change as required. Alternative tool option: fastp

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)

Inputs

ID Name Description Type
Input file: long reads Input file: long reads n/a n/a
Input file: Illumina reads R1 Input file: Illumina reads R1 n/a n/a
Input file: Illumina reads R2 Input file: Illumina reads R2 n/a n/a
adapters adapters runtime parameter for tool FastQC n/a
contaminants contaminants runtime parameter for tool FastQC n/a
limits limits runtime parameter for tool FastQC n/a
adapters adapters runtime parameter for tool FastQC n/a
contaminants contaminants runtime parameter for tool FastQC n/a
limits limits runtime parameter for tool FastQC n/a

Steps

ID Name Description
0 Input file: long reads
1 Input file: Illumina reads R1
2 Input file: Illumina reads R2
3 Nanoplot: long reads toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1
4 FastQC on R1 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
5 FastQC on R2 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
6 MultiQC: combine fastQC reports toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1

Outputs

ID Name Description Type
output_html output_html n/a
nanostats nanostats n/a
nanostats_post_filtering nanostats_post_filtering n/a
read_length read_length n/a
log_read_length log_read_length n/a
html_file html_file n/a
text_file text_file n/a
html_file html_file n/a
text_file text_file n/a
stats stats n/a
html_report html_report n/a

Version History

Version 1 (earliest) Created 8th Nov 2021 at 04:34 by Anna Syme

Added/updated 2 files


Open master c962e98
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Citation
Syme, A. (2021). Data QC. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.222.1
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Views: 1103   Downloads: 4

Created: 8th Nov 2021 at 04:34

Last updated: 9th Nov 2021 at 01:09

Last used: 2nd Dec 2022 at 12:53

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