Description

Removes host reads from short- and long-read FASTQ sequencing files

Input

name:type
description
pattern

meta

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

reads

:file

Paired or single end FASTQ files

*.{fastq,fq,fastq.gz,fq.gz}

reference_name

:string

Name of the reference to align against and thus remove mapped reads to.

reference_dir

:directory

Directory containing index file(s) corresponding to the preferred aligner (bowtie2 short reads or minimap for long reads). Note that single end data is assumed to be long reads. If you have single-end short read you must supply both the BowTie2 indices AND explicitly specify --aligner bowtie2

Output

name:type
description
pattern

fastq

meta

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.fastq.gz

:file

Cleaned FASTQ files with host reads removed

*.{fastq,fq,fastq.gz,fq.gz}

json

meta

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.json

:file

JSON report containing statistics from hostile cleaning

*.json

versions

versions.yml

:file

File containing software versions

versions.yml

Tools

hostile
MIT

Hostile: accurate host decontamination

github.com/bede/hostile 10.1093/bioinformatics/btad728
maintainer
Github user jfy133
get in touch
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