Workflow Type: Galaxy

workflow-qc-of-radseq-reads

These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using the tools from the Stacks program.

Galaxy Australia: https://usegalaxy.org.au/

Stacks: http://catchenlab.life.illinois.edu/stacks/

Inputs

  • demultiplexed reads in fastq format, in a collection
  • two adapter sequences in fasta format, for input into cutadapt

Steps and outputs

The workflow can be modified to suit your own parameters.

The workflow steps are:

  • Run FastQC to get statistics on the raw reads, send to MultiQC to create a nice output. This is tagged as "Report 1" in the Galaxy history.
  • Run Cutadapt on the reads to cut adapters - enter two files with adapter sequence at the workflow option for "Choose file containing 3' adapters". The default settings are on except that the "Maximum error rate" for the adapters is set to 0.2 instead of 0.1. Send output statistics to MulitQC, this is "Report 2" in the Galaxy history. Note that you may have different requirements here in terms of how many adapter sequences you want to enter. We recommend copying the workflow and modifying as needed.
  • Send these reads to fastp for additional filtering or trimming. Default settings are on but can be modified as needed. Send output statistics to MultiQC, this is "Report 3" in the Galaxy history.
  • The filtered and trimmed reads are then ready for the stacks workflows.

qc-wf

Inputs

ID Name Description Type
Demultiplexed reads Demultiplexed reads n/a
  • File[]

Steps

ID Name Description
1 FastQC before cutadapt toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
2 Cutadapt Remove adapters from reads. Supply two adapter.fasta files (ask sequencing provider for adapter seqs). Default settings on except max error rate changed to 0.2, and min read length set to 70 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0
3 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0
4 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0
5 fastp Additional filtering and trimming options. All defaults are on. toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0
6 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0

Outputs

ID Name Description Type
FastQC on input dataset(s): Webpage FastQC on input dataset(s): Webpage n/a
  • File
FastQC on input dataset(s): RawData FastQC on input dataset(s): RawData n/a
  • File
Cutadapt on input dataset(s): Read 1 Output Cutadapt on input dataset(s): Read 1 Output n/a
  • File
_anonymous_output_1 _anonymous_output_1 n/a
  • File
MultiQC on input dataset(s): Webpage MultiQC on input dataset(s): Webpage n/a
  • File
MultiQC on input dataset(s): Stats MultiQC on input dataset(s): Stats n/a
  • File
_anonymous_output_2 _anonymous_output_2 n/a
  • File
_anonymous_output_3 _anonymous_output_3 n/a
  • File
fastp on input dataset(s): Read 1 output fastp on input dataset(s): Read 1 output n/a
  • File
fastp on input dataset(s): HTML report fastp on input dataset(s): HTML report n/a
  • File
_anonymous_output_4 _anonymous_output_4 n/a
  • File
_anonymous_output_5 _anonymous_output_5 n/a
  • File
_anonymous_output_6 _anonymous_output_6 n/a
  • File

Version History

v1.0 (earliest) Created 31st May 2022 at 07:55 by Anna Syme

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Created: 31st May 2022 at 07:55

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