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bowtie2-build - Man Page

manual page for bowtie2-build 2.5.1


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)


comma-separated list of files with ref sequences


write bt2 data to files with this dir/basename

*** Bowtie 2 indexes will work with Bowtie v1.2.3 and later. *** Options:


reference files are Fasta (default)


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


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


use the debug binary; slower, assertions enabled


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


log the issued command


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


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)


disable diff-cover (algorithm becomes quadratic)


don't build .3/.4 index files


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


verbose output (for debugging)


print this message and quit


print version information and quit


January 2024 bowtie2-build 2.5.1