bowtie-build1

Building a colorspace index for bowtie

Usage

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

Overview

`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 2^offRate 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}

Releases

7 releases since Debian 7 (Wheezy); the text changed 6 times.

--large-index since Debian 8 (Jessie); --threads since Debian 10 (Buster).

-B until Debian 7 (Wheezy).