NAME¶

SYNOPSIS¶

DESCRIPTION¶

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

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 24 September 2018 Compiler: gcc version 8.2.0 (Debian 8.2.0-7) Options: -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DPOPCNT_CAPABILITY Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}