.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.1.
.TH KRAKEN "1" "September 2015" "kraken 0.10.5~beta" "User Commands"
.SH NAME
kraken \- assigning taxonomic labels to short DNA sequences
.SH SYNOPSIS
.B kraken
[\fI\,options\/\fR] \fI\,<filename(s)>\/\fR
.SH OPTIONS
.TP
\fB\-\-db\fR NAME
Name for Kraken DB
(default: none)
.TP
\fB\-\-threads\fR NUM
Number of threads (default: 1)
.TP
\fB\-\-fasta\-input\fR
Input is FASTA format
.TP
\fB\-\-fastq\-input\fR
Input is FASTQ format
.TP
\fB\-\-gzip\-compressed\fR
Input is gzip compressed
.TP
\fB\-\-bzip2\-compressed\fR
Input is bzip2 compressed
.TP
\fB\-\-quick\fR
Quick operation (use first hit or hits)
.TP
\fB\-\-min\-hits\fR NUM
In quick op., number of hits req'd for classification
NOTE: this is ignored if \fB\-\-quick\fR is not specified
.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\-\-only\-classified\-output\fR
Print no Kraken output for unclassified sequences
.TP
\fB\-\-preload\fR
Loads DB into memory before classification
.TP
\fB\-\-paired\fR
The two filenames provided are paired\-end reads
.TP
\fB\-\-check\-names\fR
Ensure each pair of reads have names that agree
with each other; ignored if \fB\-\-paired\fR is not specified
.TP
\fB\-\-help\fR
Print this message
.TP
\fB\-\-version\fR
Print version information
.PP
If none of the *\-input or *\-compressed flags are specified, and the
file is a regular file, automatic format detection is attempted.