Reference

bowtie(1)

ultrafast memory-efficient short read aligner

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 Thu, 25 Jan 2024 12:27:31 +0100 Compiler: gcc version 13.2.0 Options: -O3 -Wl,--hash-style=both -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -Wl,-z,relro -Wl,-z,now Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

History

--help since Debian 10 (Buster); -h since Debian 10 (Buster).

--al until Debian 9 (Stretch); --best until Debian 9 (Stretch); --chunkmbs until Debian 9 (Stretch); --col-cqual until Debian 9 (Stretch); --col-cseq until Debian 9 (Stretch); --col-keepends until Debian 9 (Stretch); --fullref until Debian 9 (Stretch); --integer-quals until Debian 9 (Stretch); --large-index until Debian 9 (Stretch); --mapq until Debian 9 (Stretch); --max until Debian 9 (Stretch); --maxbts until Debian 9 (Stretch); --mm until Debian 9 (Stretch); --nomaqround until Debian 9 (Stretch); --pairtries until Debian 9 (Stretch); --phred33-quals until Debian 9 (Stretch); --phred64-quals until Debian 9 (Stretch); --quiet until Debian 9 (Stretch); --refidx until Debian 9 (Stretch); --refout until Debian 9 (Stretch); --sam-RG until Debian 9 (Stretch); --sam-nohead until Debian 9 (Stretch); --sam-nosq until Debian 9 (Stretch); --seed until Debian 9 (Stretch); --shmem until Debian 9 (Stretch); --snpfrac until Debian 9 (Stretch); --snpphred until Debian 9 (Stretch); --solexa-quals until Debian 9 (Stretch); --solexa1.3-quals until Debian 9 (Stretch); --strata until Debian 9 (Stretch); --suppress until Debian 9 (Stretch); --un until Debian 9 (Stretch); --verbose until Debian 9 (Stretch); --version until Debian 9 (Stretch); -C until Debian 9 (Stretch); -M until Debian 9 (Stretch); -c until Debian 9 (Stretch); -f until Debian 9 (Stretch); -k until Debian 9 (Stretch); -m until Debian 9 (Stretch); -q until Debian 9 (Stretch); -r until Debian 9 (Stretch); -v until Debian 9 (Stretch).