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)

       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>)

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

       -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  September  2021  Compiler:  gcc  version  11.2.0  (Ubuntu
       11.2.0-7ubuntu2)  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}