bowtie2-build - Man Page

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

Bowtie 2 version 2.5.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)

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 will work with Bowtie v1.2.3 and later. *** Options:

-f

reference files are Fasta (default)

-c

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

--large-index

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

--debug

use the debug binary; slower, assertions enabled

--sanitized

use sanitized binary; slower, uses ASan and/or UBSan

--verbose

log the issued command

-a/--noauto

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

-p/--packed

use packed strings internally; slower, less memory

--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 index files

-3/--justref

just build .3/.4 index files

-o/--offrate <int>

SA is sampled every 2^<int> BWT chars (default: 5)

-t/--ftabchars <int>

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

--threads <int>

# of threads

--seed <int>

seed for random number generator

-q/--quiet

verbose output (for debugging)

--h/--help

print this message and quit

--version

print version information and quit