NAME¶

bowtie2-build - building a colorspace index for bowtie2

SYNOPSIS¶

bowtie2-build [ options]* <reference_in> <bt2_index_base>

DESCRIPTION¶

Bowtie 2 version 2.0.0-beta6 by Ben Langmead (blangmea@jhsph.edu)

reference_in

comma-separated list of files with ref sequences

bt2_index_base

write .bt2 data to files with this dir/basename

*** Bowtie 2 indexes work only with v2 (not v1). Likewise for v1 indexes. *** Options:

-f

reference files are Fasta (default)

-c

reference sequences given on cmd line (as <seq_in>)

-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.bt2 (packed reference) portion

-3/--justref

just build .3/.4.bt2 (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)

--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 lxcsid Fri Jun 1 20:11:23 UTC 2012 Compiler: gcc version 4.7.0 (Debian 4.7.0-8) Options: -O3 -m64 -msse2 -funroll-loops -g3 Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}