Man page - bowtie2-build-s(1)

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Manual

BOWTIE2-BUILD-S

NAME
SYNOPSIS
DESCRIPTION
OPTIONS

NAME

bowtie2-build-s - building a colorspace index for bowtie2

SYNOPSIS

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

DESCRIPTION

Bowtie 2 version 2.5.4 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>)

-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 2ˆ<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