host-contamination-removal-short-reads/main
v0.3 (latest)

v0.3 (latest)

v0.2

v0.1 (earliest)

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Run on Galaxy

Workflow Type: Galaxy

Tests Passing

This workflow takes paired-end Illumina fastq(.gz) files and runs Bowtie to map the reads against a reference genome (human, by default) and keep only the reads that do not align. MultiQC is used to aggregate the mapping reports.

SEEK ID: https://workflowhub.eu/workflows/2026?version=3

Inputs

ID	Name	Description	Type
Contaminant Reference Genome	#main/Host/Contaminant Reference Genome	Reads not mapping to this reference genome will be kept.	string
Short-reads	#main/Short-reads	Short-reads as a paired-end collection of fastqsanger(.gz) files	array containing File

Steps

ID	Name	Description
2	Bowtie2	Map the reads against a reference genome and output the ones not mapping the reference genome toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0
3	MultiQC	Aggregation of the mapping statistics for all samples toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0

Outputs

ID	Name	Description	Type
Bowtie2 Mapping Statistics	#main/Bowtie2 Mapping Statistics	n/a	File
Contamination Filtered Reads	#main/Contamination Filtered Reads	n/a	File
MultiQC HTML Report	#main/MultiQC HTML Report	n/a	File

Version History

v0.3 (latest) Created 21st Jan 2026 at 03:01 by WorkflowHub Bot

Updated to v0.3

Frozen v0.3 cb3aedc

v0.2 Created 9th Dec 2025 at 03:02 by WorkflowHub Bot

Updated to v0.2

Frozen v0.2 db6c354

v0.1 (earliest) Created 6th Dec 2025 at 03:02 by WorkflowHub Bot

Updated to v0.1

Frozen v0.1 25561f7

Creators and Submitter

Creators

Submitter

WorkflowHub Bot

License

MIT License (MIT)

Activity

Views: 1111 Downloads: 3573 Runs: 2

Created: 6th Dec 2025 at 03:01

host-contamination-removal-short-reads/main v0.3 (latest) v0.3 (latest) v0.2 v0.1 (earliest)