kraken2

kraken2 [options] <filename(s)>

--db NAME

Name for Kraken 2 DB (default: none)

--threads NUM

Number of threads (default: 1)

--quick

Quick operation (use first hit or hits)

--unclassified-out FILENAME

Print unclassified sequences to filename

--classified-out FILENAME

Print classified sequences to filename

--output FILENAME

Print output to filename (default: stdout); "-" will suppress normal output

--confidence FLOAT

Confidence score threshold (default: 0.0); must be in [0, 1].

--minimum-base-quality NUM

Minimum base quality used in classification (def: 0, only effective with FASTQ input).

--report FILENAME

Print a report with aggregrate counts/clade to file

--use-mpa-style

With --report, format report output like Kraken 1's kraken-mpa-report

--report-zero-counts

With --report, report counts for ALL taxa, even if counts are zero

--memory-mapping

Avoids loading database into RAM

--paired

The filenames provided have paired-end reads

--use-names

Print scientific names instead of just taxids

--gzip-compressed

Input files are compressed with gzip

--bzip2-compressed

Input files are compressed with bzip2

--help

Print this message

--version

Print version information

If none of the *-compressed flags are specified, and the filename provided is a regular file, automatic format detection is attempted.

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.