.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH BOWTIE-ALIGN-S "1" "September 2018" "bowtie-align-s version 1.2.2" "User Commands"
.SH NAME
bowtie-align-s \- ultrafast memory-efficient short read aligner
.SH DESCRIPTION
usage: bowtie [\-h] [\-b | \fB\-i]\fR [\-\-verbose] [\-\-debug] [\-\-large\-index]
.IP
[\-\-index INDEX]
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.HP
\fB\-b\fR, \fB\-\-build\fR
.HP
\fB\-i\fR, \fB\-\-inspect\fR
.HP
\fB\-\-verbose\fR
.HP
\fB\-\-debug\fR
.HP
\fB\-\-large\-index\fR
.HP
\fB\-\-index\fR INDEX
.PP
64\-bit
Built on Debian\-reproducible
Wed, 05 Sep 2018 14:34:56 +0000
Compiler: gcc version 8.2.0
Options: \fB\-O3\fR  \fB\-Wl\fR,\-\-hash\-style=both \fB\-DWITH_TBB\fR \fB\-Wdate\-time\fR \fB\-D_FORTIFY_SOURCE\fR=\fI\,2\/\fR \fB\-g\fR \fB\-O2\fR \fB\-fdebug\-prefix\-map=\fR.=. \fB\-fstack\-protector\-strong\fR \fB\-Wformat\fR \fB\-Werror\fR=\fI\,format\-security\/\fR  \fB\-g\fR \fB\-O2\fR \fB\-fdebug\-prefix\-map=\fR.=. \fB\-fstack\-protector\-strong\fR \fB\-Wformat\fR \fB\-Werror\fR=\fI\,format\-security\/\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}