Provided by: hisat2_2.2.1-4_amd64
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 (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 <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 14 October 2022 Compiler: gcc version 12.2.0 (Ubuntu 12.2.0-9ubuntu1) 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}