NAME

       bowtie-align-s - ultrafast memory-efficient short read aligner

DESCRIPTION

       usage: bowtie [-h] [--verbose] [--debug] [--large-index]

   options:
       -h, --help
              show this help message and exit

       --verbose

       --debug

       --large-index

       64-bit Built on Debian-reproducible Tue, 09 Dec 2025 23:19:38 +0000 Compiler: gcc version 15.2.0 Options:
       -O3     -Wl,--hash-style=both     -DPOPCNT_CAPABILITY     -Wdate-time    -D_FORTIFY_SOURCE=3    -g    -O2
       -Werror=implicit-function-declaration        -fno-omit-frame-pointer         -mno-omit-leaf-frame-pointer
       -ffile-prefix-map=.=.   -flto=auto  -ffat-lto-objects  -fstack-protector-strong  -fstack-clash-protection
       -Wformat -Werror=format-security -fcf-protection  -fdebug-prefix-map=.=/usr/src/bowtie-1.3.1-3build1   -g
       -O2     -fno-omit-frame-pointer     -mno-omit-leaf-frame-pointer     -ffile-prefix-map=.=.     -flto=auto
       -ffat-lto-objects  -fstack-protector-strong  -fstack-clash-protection  -Wformat   -Werror=format-security
       -fcf-protection  -fdebug-prefix-map=.=/usr/src/bowtie-1.3.1-3build1  -std=c++03  -Wl,-Bsymbolic-functions
       -Wl,--package-metadata={%22type%22:%22deb%22%2C%22os%22:%22ubuntu%22%2C%22name%22:%22bowtie%22%2C%22version%22:%221.3.1-3build1%22%2C%22architecture%22:%22amd64%22}
       -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now Sizeof {int, long, long long, void*, size_t, off_t}:
       {4, 8, 8, 8, 8, 8}

bowtie-align-s version 1.3.1                      December 2025                                BOWTIE-ALIGN-S(1)