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nf-core/disambiguate @ 0.0.0-0c7146d

Disambiguates reads aligned to two different organisms (e.g. human and mouse) from the same source of FASTQ files. Useful in explant RNA/DNA-Seq workflows where reads from two species are present. For reads aligned to both organisms, the algorithm compares alignment quality scores to determine the most likely species of origin. Produces four BAM files (uniquely assigned to species A or B, ambiguous for species A or B) and a summary file.

disambiguation xenograft explant rna-seq alignment bam
Latest version: 0.0.0-0c7146d
Total downloads: 1
Source: nf-core/modules
Authors: @ctuni
Maintainers: @ctuni

Summary

Disambiguates reads aligned to two different organisms (e.g. human and mouse) from the same source of FASTQ files. Useful in explant RNA/DNA-Seq workflows where reads from two species are present. For reads aligned to both organisms, the algorithm compares alignment quality scores to determine the most likely species of origin. Produces four BAM files (uniquely assigned to species A or B, ambiguous for species A or B) and a summary file.

Get started

Add the following snippet to your workflow script to include this module.

include { DISAMBIGUATE } from 'nf-core/disambiguate'

License

MIT License

Process
Name DISAMBIGUATE
Input 1 channel
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
bam_a file

BAM file with alignments to species A (e.g. human). Mandatory.

 *.{bam}
bam_b file

BAM file with alignments to species B (e.g. mouse). Mandatory.

 *.{bam}
Output 6 channels
#1 summary tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*_summary.txt file

Summary of read counts uniquely assigned to species A, species B, and ambiguous reads.

 *_summary.txt
#2 ambiguous_bam_a tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*ambiguousSpeciesA.bam file

Reads aligned to species A that also aligned to species B but could not be uniquely assigned.

 *ambiguousSpeciesA.bam
#3 ambiguous_bam_b tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*ambiguousSpeciesB.bam file

Reads aligned to species B that also aligned to species A but could not be uniquely assigned.

 *ambiguousSpeciesB.bam
#4 disambiguated_bam_a tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*disambiguatedSpeciesA.bam file

Reads uniquely assigned to species A.

 *disambiguatedSpeciesA.bam
#5 disambiguated_bam_b tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*disambiguatedSpeciesB.bam file

Reads uniquely assigned to species B.

 *disambiguatedSpeciesB.bam
#6 versions_ngs_disambiguate tuple
${task.process} string

The name of the process
ngs-disambiguate string

The name of the tool
2018.05.03 string

The expression to obtain the version of the tool
Tool Description Homepage
ngs-disambiguate Disambiguation algorithm for reads aligned to two different organisms using Tophat, Hisat2, BWA or STAR alignments. https://github.com/AstraZeneca-NGS/disambiguate
Version 0.0.0-0c7146d
Commit ID 135d883a43b1a2324b4112cd270cf22e20835533
Release Date 08 Apr 2026 18:36:11 (UTC)
Download URL https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fdisambiguate/0.0.0-0c7146d/download
OCI Store URL https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/disambiguate/blobs/sha256:c0ce35c8dfce8cf847f5ccc2dd28fdda23b36cea5cc5e3baf51906532508c4ee
Size 2.9 KB
Checksum sha256:c0ce35c8dfce8cf847f5ccc2dd28fdda23b36cea5cc5e3baf51906532508c4ee
Downloads 1
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