.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.9.
.TH BOWTIE2-BUILD "1" "June 2012" "bowtie2-build version 2.0.0-beta6" "User Commands"
.SH NAME
bowtie2-build \- building a colorspace index for bowtie2
.SH SYNOPSIS
.B bowtie2-build
[\fIoptions\fR]\fI* <reference_in> <bt2_index_base>\fR
.SH DESCRIPTION
Bowtie 2 version 2.0.0\-beta6 by Ben Langmead (blangmea@jhsph.edu)
.TP
reference_in
comma\-separated list of files with ref sequences
.TP
bt2_index_base
write .bt2 data to files with this dir/basename
.PP
*** Bowtie 2 indexes work only with v2 (not v1).  Likewise for v1 indexes. ***
Options:
.TP
\fB\-f\fR
reference files are Fasta (default)
.TP
\fB\-c\fR
reference sequences given on cmd line (as <seq_in>)
.TP
\fB\-a\fR/\-\-noauto
disable automatic \fB\-p\fR/\-\-bmax/\-\-dcv memory\-fitting
.TP
\fB\-p\fR/\-\-packed
use packed strings internally; slower, uses less mem
.TP
\fB\-\-bmax\fR <int>
max bucket sz for blockwise suffix\-array builder
.TP
\fB\-\-bmaxdivn\fR <int>
max bucket sz as divisor of ref len (default: 4)
.TP
\fB\-\-dcv\fR <int>
diff\-cover period for blockwise (default: 1024)
.TP
\fB\-\-nodc\fR
disable diff\-cover (algorithm becomes quadratic)
.TP
\fB\-r\fR/\-\-noref
don't build .3/.4.bt2 (packed reference) portion
.TP
\fB\-3\fR/\-\-justref
just build .3/.4.bt2 (packed reference) portion
.TP
\fB\-o\fR/\-\-offrate <int>
SA is sampled every 2^offRate BWT chars (default: 5)
.TP
\fB\-t\fR/\-\-ftabchars <int>
# of chars consumed in initial lookup (default: 10)
.TP
\fB\-\-seed\fR <int>
seed for random number generator
.TP
\fB\-q\fR/\-\-quiet
verbose output (for debugging)
.TP
\fB\-h\fR/\-\-help
print detailed description of tool and its options
.TP
\fB\-\-usage\fR
print this usage message
.TP
\fB\-\-version\fR
print version information and quit
.PP
64\-bit
Built on lxcsid
Fri Jun  1 20:11:23 UTC 2012
Compiler: gcc version 4.7.0 (Debian 4.7.0\-8)
Options: \fB\-O3\fR \fB\-m64\fR \fB\-msse2\fR \fB\-funroll\-loops\fR \fB\-g3\fR
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}