Description

Extract reads classified at any user-specified taxonomy IDs.

Input

Name (Type)
Description
Pattern

meta (map)

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

taxid (string)

A list of taxid separated by spaces

classified_reads_assignment (file)

A file contains the taxonomic classification of each input read.

*.{classifiedreads.txt}

classified_reads_fastq (file)

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

*.{fastq.gz}

report (file)

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

*.{report.txt}

Output

Name (Type)
Description
Pattern

meta (map)

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

extracted_kraken2_reads (file)

Reads assigned to a taxid list.

*.{fastq,fasta}

versions (file)

File containing software versions

versions.yml
maintainer
Github user LilyAnderssonLee
get in touch
Ask a question on Slack Open an issue on GitHub

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