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HISAT2-BUILD-S(1) User Commands HISAT2-BUILD-S(1)


hisat2-build-s - HISAT2 indexer, small index binary


hisat2-build [options]* <reference_in> <ht2_index_base>


HISAT2 version 2.2.0 by Daehwan Kim (,
comma-separated list of files with ref sequences
write ht2 data to files with this dir/basename


reference sequences given on cmd line (as <reference_in>)
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)
disable diff-cover (algorithm becomes quadratic)
don't build .3/.4.ht2 (packed reference) portion
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
disable verbose output (for debugging)
print detailed description of tool and its options
print this usage message
print version information and quit

64-bit Built on Debian 06 May 2020 Compiler: gcc version 9.3.0 (Debian 9.3.0-11) 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}

May 2020 hisat2-build-s version 2.2.0