.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH BOWTIE-BUILD "1" "January 2024" "bowtie-build version 1.3.1" "User Commands"
.SH NAME
bowtie-build \- building a colorspace index for bowtie
.SH SYNOPSIS
.B bowtie-build
[\fI\,options\/\fR]\fI\,* <reference_in> <ebwt_outfile_base>\/\fR
.SH DESCRIPTION
.TP
reference_in
comma\-separated list of files with ref sequences
.TP
ebwt_outfile_base
write Ebwt data to files with this dir/basename
.SH 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\-\-large\-index\fR
force generated index to be 'large', even if ref
has fewer than 4 billion nucleotides
.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.ebwt (packed reference) portion
.TP
\fB\-3\fR/\-\-justref
just build .3/.4.ebwt (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\-\-threads\fR <int>
# of threads
.TP
\fB\-\-ntoa\fR
convert Ns in reference to As
.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 Debian\-reproducible
Thu, 25 Jan 2024 12:27:31 +0100
Compiler: gcc version 13.2.0
Options: \fB\-O3\fR \fB\-Wl\fR,\-\-hash\-style=both \fB\-DPOPCNT_CAPABILITY\fR \fB\-Wdate\-time\fR \fB\-D_FORTIFY_SOURCE\fR=\fI\,2\/\fR \fB\-g\fR \fB\-O2\fR \fB\-ffile\-prefix\-map=\fR.=. \fB\-fstack\-protector\-strong\fR \fB\-fstack\-clash\-protection\fR \fB\-Wformat\fR \fB\-Werror\fR=\fI\,format\-security\/\fR \fB\-fcf\-protection\fR  \fB\-g\fR \fB\-O2\fR \fB\-ffile\-prefix\-map=\fR.=. \fB\-fstack\-protector\-strong\fR \fB\-fstack\-clash\-protection\fR \fB\-Wformat\fR \fB\-Werror\fR=\fI\,format\-security\/\fR \fB\-fcf\-protection\fR \fB\-std\fR=\fI\,c\/\fR++03 \fB\-Wl\fR,\-z,relro \fB\-Wl\fR,\-z,now
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}