NAME

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

SYNOPSIS

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

DESCRIPTION

       HISAT2       version       2.1.0       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>)

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

       -p     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

       --seed <int>
              seed for random number generator

       -q/--quiet
              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 11 February 2020  Compiler:  gcc  version  9.2.1  20200203  (Ubuntu
       9.2.1-28ubuntu1)  Options: -O3   -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 Sizeof
       {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}