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.

Inputs

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

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

Name

Description

Type

Demultiplexed reads

n/a

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