Trim and filter reads - fastp
Version 1

Workflow Type: Galaxy

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


  • 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)


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


ID Name Description
0 Illumina reads R1
1 Illumina reads R2
2 long reads
3 fastp on short reads
4 fastp on long reads


ID Name Description Type
out1 out1 n/a
out2 out2 n/a
report_html report_html n/a
report_json report_json n/a
out1 out1 n/a
report_html report_html n/a
report_json report_json n/a

Version History

Version 1 (earliest) Created 8th Nov 2021 at 04:56 by Anna Syme

Added/updated 2 files

Open master 88e7c49
help Creators and Submitter
Syme, A. (2021). Trim and filter reads - fastp. WorkflowHub.

Views: 1908   Downloads: 5

Created: 8th Nov 2021 at 04:56

Last updated: 9th Nov 2021 at 01:11

Last used: 2nd Dec 2022 at 11:57

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