NAME
hisat2-build-s - HISAT2 indexer, small index binary
SYNOPSIS
hisat2-build [options]* <reference_in> <ht2_index_base>
DESCRIPTION
HISAT2 version 2.2.1 by Daehwan Kim ([email protected], http://www.ccb.jhu.edu/people/infphilo)
- reference_in
-
comma-separated list of files with ref sequences
- hisat2_index_base
-
write ht2 data to files with this dir/basename
OPTIONS
- -c
-
reference sequences given on cmd line (as <reference_in>)
- -a/--noauto
-
disable automatic -p/--bmax/--dcv memory-fitting
- -p <int>
-
number of threads
- --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.ht2 (packed reference) portion
- -3/--justref
-
just build .3/.4.ht2 (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)
- --localoffrate <int>
-
SA (local) is sampled every 2^offRate BWT chars (default: 3)
- --localftabchars <int>
-
# of chars consumed in initial lookup in a local index (default: 6)
- --snp <path>
-
SNP file name
- --haplotype <path>
-
haplotype file name
- --ss <path>
-
Splice site file name
- --exon <path>
-
Exon file name
- --repeat-ref <path>
-
Repeat reference file name
- --repeat-info <path>
-
Repeat information file name
- --repeat-snp <path>
-
Repeat snp file name
- --repeat-haplotype <path>
-
Repeat haplotype file name
- --seed <int>
-
seed for random number generator
- -q/--quiet
-
disable 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 28 March 2025 Compiler: gcc version 14.2.0 (Debian 14.2.0-19) Options: -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}