.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.1.
.TH KRAKEN-BUILD "1" "September 2015" "kraken-build 0.10.5~beta" "User Commands"
.SH NAME
kraken-build \- assigning taxonomic labels to short DNA sequences
.SH SYNOPSIS
.B kraken-build
[\fI\,task option\/\fR] [\fI\,options\/\fR]
.SH DESCRIPTION
.SS "Task options (exactly one must be selected):"
.TP
\fB\-\-download\-taxonomy\fR
Download NCBI taxonomic information
.TP
\fB\-\-download\-library\fR TYPE
Download partial library
(TYPE = one of "bacteria", "plasmids",
"viruses", "human")
.TP
\fB\-\-add\-to\-library\fR FILE
Add FILE to library
.TP
\fB\-\-build\fR
Create DB from library
(requires taxonomy d/l'ed and at least one file
in library)
.TP
\fB\-\-rebuild\fR
Create DB from library like \fB\-\-build\fR, but remove
existing non\-library/taxonomy files before build
.TP
\fB\-\-clean\fR
Remove unneeded files from a built database
.TP
\fB\-\-shrink\fR NEW_CT
Shrink an existing DB to have only NEW_CT k\-mers
.TP
\fB\-\-standard\fR
Download and create default database
.TP
\fB\-\-upgrade\fR
Upgrade an existing older database to use scrambled
minimizer ordering (see README for details)
.TP
\fB\-\-help\fR
Print this message
.TP
\fB\-\-version\fR
Print version information
.SH OPTIONS
.TP
\fB\-\-db\fR NAME
Kraken DB/library name (mandatory except for
\fB\-\-help\fR/\-\-version)
.TP
\fB\-\-threads\fR #
Number of threads (def: 1)
.TP
\fB\-\-new\-db\fR NAME
New Kraken DB name (shrink task only; mandatory
for shrink task)
.TP
\fB\-\-kmer\-len\fR NUM
K\-mer length in bp (build/shrink tasks only;
def: 31)
.TP
\fB\-\-minimizer\-len\fR NUM
Minimizer length in bp (build/shrink tasks only;
def: 15)
.TP
\fB\-\-jellyfish\-hash\-size\fR STR
Pass a specific hash size argument to jellyfish
when building database (build task only)
.TP
\fB\-\-max\-db\-size\fR SIZE
Shrink the DB before full build, making sure
database and index together use <= SIZE gigabytes
(build task only)
.TP
\fB\-\-shrink\-block\-offset\fR NUM
When shrinking, select the k\-mer that is NUM
positions from the end of a block of k\-mers
(default: 1)
.TP
\fB\-\-work\-on\-disk\fR
Perform most operations on disk rather than in
RAM (will slow down build in most cases)