Extract reads classified at any user-specified taxonomy IDs.
meta
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
taxid
A list of taxid separated by spaces
classified_reads_assignment
A file contains the taxonomic classification of each input read.
*.{classifiedreads.txt}
classified_reads_fastq
Classified reads as belonging to any of the taxa on the kraken2 database.
*.{fastq.gz}
report
Optional Kraken2 report containing stats about classified and not classifed reads.
*.{report.txt}
extracted_kraken2_reads
Reads assigned to a taxid list.
*.{fastq,fasta}
versions
File containing software versions
versions.yml
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.