hisat2-build - HISAT2 indexer, wrapper script
hisat2-build [options]* <reference_in>
<ht2_index_base>
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
- -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 25 February 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, 8, 8, 8, 8, 8}