.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH KRAKEN2 "1" "March 2019" "kraken2 2.0.7~beta" "User Commands"
.SH NAME
kraken2 \- assigning taxonomic labels to short DNA sequences
.SH SYNOPSIS
.B kraken2
[\fI\,options\/\fR] \fI\,<filename(s)>\/\fR
.SH OPTIONS
.TP
\fB\-\-db\fR NAME
Name for Kraken 2 DB
(default: none)
.TP
\fB\-\-threads\fR NUM
Number of threads (default: 1)
.TP
\fB\-\-quick\fR
Quick operation (use first hit or hits)
.TP
\fB\-\-unclassified\-out\fR FILENAME
Print unclassified sequences to filename
.TP
\fB\-\-classified\-out\fR FILENAME
Print classified sequences to filename
.TP
\fB\-\-output\fR FILENAME
Print output to filename (default: stdout); "\-" will
suppress normal output
.TP
\fB\-\-confidence\fR FLOAT
Confidence score threshold (default: 0.0); must be
in [0, 1].
.TP
\fB\-\-minimum\-base\-quality\fR NUM
Minimum base quality used in classification (def: 0,
only effective with FASTQ input).
.TP
\fB\-\-report\fR FILENAME
Print a report with aggregrate counts/clade to file
.TP
\fB\-\-use\-mpa\-style\fR
With \fB\-\-report\fR, format report output like Kraken 1's
kraken\-mpa\-report
.TP
\fB\-\-report\-zero\-counts\fR
With \fB\-\-report\fR, report counts for ALL taxa, even if
counts are zero
.TP
\fB\-\-memory\-mapping\fR
Avoids loading database into RAM
.TP
\fB\-\-paired\fR
The filenames provided have paired\-end reads
.TP
\fB\-\-use\-names\fR
Print scientific names instead of just taxids
.TP
\fB\-\-gzip\-compressed\fR
Input files are compressed with gzip
.TP
\fB\-\-bzip2\-compressed\fR
Input files are compressed with bzip2
.TP
\fB\-\-help\fR
Print this message
.TP
\fB\-\-version\fR
Print version information
.PP
If none of the *\-compressed flags are specified, and the filename provided
is a regular file, automatic format detection is attempted.
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.