Man page - bowtie-build-debug(1)

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Package: bowtie
apt-get install bowtie

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bowtie

Manual

BOWTIE-BUILD

NAME
SYNOPSIS
DESCRIPTION
OPTIONS

NAME

bowtie-build - building a colorspace index for bowtie

SYNOPSIS

bowtie-build [ options ] * <reference_in> <ebwt_outfile_base>

DESCRIPTION

reference_in

comma-separated list of files with ref sequences

ebwt_outfile_base

write Ebwt data to files with this dir/basename

OPTIONS

	-f		reference files are Fasta (default)
	-c		reference sequences given on cmd line (as <seq_in>)

--large-index

force generated index to be ’large’, even if ref has fewer than 4 billion nucleotides

-a /--noauto

disable automatic -p /--bmax/--dcv memory-fitting

-p /--packed

use packed strings internally; slower, uses less mem

--bmax <int>

max bucket sz for blockwise suffix-array builder

--bmaxdivn <int>

max bucket sz as divisor of ref len (default: 4)

--dcv <int>

diff-cover period for blockwise (default: 1024)

--nodc

disable diff-cover (algorithm becomes quadratic)

-r /--noref

don’t build .3/.4.ebwt (packed reference) portion

-3 /--justref

just build .3/.4.ebwt (packed reference) portion

-o /--offrate <int>

SA is sampled every 2ˆoffRate BWT chars (default: 5)

-t /--ftabchars <int>

# of chars consumed in initial lookup (default: 10)

--threads <int>

# of threads

--ntoa

convert Ns in reference to As

--seed <int>

seed for random number generator

-q /--quiet

verbose output (for debugging)

-h /--help

print detailed description of tool and its options

--usage

print this usage message

--version

print version information and quit

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}