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

NAME

hisat2-build - HISAT2 indexer, wrapper script

SYNOPSIS

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

DESCRIPTION

HISAT2 version 2.2.1 by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo)

comma-separated list of files with ref sequences
write ht2 data to files with this dir/basename

OPTIONS

reference sequences given on cmd line (as <reference_in>)
force generated index to be 'large', even if ref has fewer than 4 billion nucleotides
disable automatic -p/--bmax/--dcv memory-fitting
number of threads
max bucket sz for blockwise suffix-array builder
max bucket sz as divisor of ref len (default: 4)
diff-cover period for blockwise (default: 1024)
disable diff-cover (algorithm becomes quadratic)
don't build .3/.4.ht2 (packed reference) portion
-3/--justref
just build .3/.4.ht2 (packed reference) portion
SA is sampled every 2^offRate BWT chars (default: 5)
# of chars consumed in initial lookup (default: 10)
SA (local) is sampled every 2^offRate BWT chars (default: 3)
# of chars consumed in initial lookup in a local index (default: 6)
SNP file name
haplotype file name
Splice site file name
Exon file name
Repeat reference file name
Repeat information file name
Repeat snp file name
Repeat haplotype file name
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

32-bit Built on Debian 22 January 2023 Compiler: gcc version 12.2.0 (Debian 12.2.0-14) 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, 4, 8, 4, 4, 8}

January 2023 hisat2-build version 2.2.1