Description

Extract reads classified at any user-specified taxonomy IDs.

Input

name:type
description
pattern

taxid{:bash}

:string

A list of taxid separated by spaces

meta{:bash}

:map

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

classified_reads_assignment{:bash}

:file

A file contains the taxonomic classification of each input read.

*.{classifiedreads.txt}

meta{:bash}

:map

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

classified_reads_fastq{:bash}

:file

Classified reads as belonging to any of the taxa on the kraken2 database.

*.{fastq.gz}

meta{:bash}

:map

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

report{:bash}

:file

Optional Kraken2 report containing stats about classified and not classified reads.

*.{report.txt}

Output

name:type
description
pattern

extracted_kraken2_reads{:bash}

meta{:bash}

:map

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

*.{fastq.gz,fasta.gz}{:bash}

:file

Reads assigned to a taxid list.

*.{fastq.gz,fasta.gz}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

krakentools
GPL v3

KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.

github.com/jenniferlu717/KrakenTools github.com/jenniferlu717/KrakenTools?tab=readme-ov-file#extract_kraken_readspy https://github.com/jenniferlu717/KrakenTools 10.1038/s41596-022-00738-y
maintainer
Github user LilyAnderssonLee
get in touch
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