Trim and filter reads

Trim and filter reads; can run alone or as part of a combined workflow for large genome assembly.

What it does: Trims and filters raw sequence reads according to specified settings.
Inputs: Long reads (format fastq); Short reads R1 and R2 (format fastq)
Outputs: Trimmed and filtered reads: fastp_filtered_long_reads.fastq.gz (But note: no trimming or filtering is on by default), fastp_filtered_R1.fastq.gz, fastp_filtered_R2.fastq.gz
Reports: fastp report on long reads, html; fastp report on short reads, html
Tools used: fastp (Note. The latest version (0.20.1) of fastp has an issue displaying plot results. Using version 0.19.5 here instead until this is rectified).
Input parameters: None required, but recommend removing the long reads from the workflow if not using any trimming/filtering settings.

Workflow steps:

Long reads: fastp settings:

These settings have been changed from the defaults (so that all filtering and trimming settings are now disabled).
Adapter trimming options: Disable adapter trimming: yes
Filter options: Quality filtering options: Disable quality filtering: yes
Filter options: Length filtering options: Disable length filtering: yes
Read modification options: PolyG tail trimming: Disable
Output options: output JSON report: yes

Short reads: fastp settings:

adapter trimming (default setting: adapters are auto-detected)
quality filtering (default: phred quality 15), unqualified bases limit (default = 40%), number of Ns allowed in a read (default = 5)
length filtering (default length = min 15)
polyG tail trimming (default = on for NextSeq/NovaSeq data which is auto detected)
Output options: output JSON report: yes

Options:

Change any settings in fastp for any of the input reads.
Adapter trimming: input the actual adapter sequences. (Alternative tool for long read adapter trimming: Porechop.)
Trimming n bases from ends of reads if quality less than value x (Alternative tool for trimming long reads: NanoFilt.)
Discard post-trimmed reads if length is < x (e.g. for long reads, 1000 bp)
Example filtering/trimming that you might do on long reads: remove adapters (can also be done with Porechop), trim bases from ends of the reads with low quality (can also be done with NanoFilt), after this can keep only reads of length x (e.g. 1000 bp)

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)

Inputs

ID	Name	Description	Type
Illumina reads R1	Illumina reads R1	n/a	File
Illumina reads R2	Illumina reads R2	n/a	File
long reads	long reads	n/a	File

Steps

ID	Name	Description
3	fastp on short reads	toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1
4	fastp on long reads	toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1

Outputs

ID	Name	Description	Type
fastp filtered R2 reads	fastp filtered R2 reads	n/a	File
fastp report on short reads html	fastp report on short reads html	n/a	File
fastp filtered R1 reads	fastp filtered R1 reads	n/a	File
fastp report on short reads json	fastp report on short reads json	n/a	File
fastp report on long reads html	fastp report on long reads html	n/a	File
fastp filtered long reads	fastp filtered long reads	n/a	File
fastp report on long reads json	fastp report on long reads json	n/a	File

Trim and filter reads - fastp
Version 1