Provided by: mhap_1.6+dfsg-1_all 
NAME
mhap - probabilistic sequence overlapping
DESCRIPTION
Please set the -s or the -p options. See options below: MHAP: MinHash Alignment Protocol. A tool for
finding overlaps of long-read sequences (such as PacBio or Nanopore) in bioinformatics.
Version: 1.6, Build time: 09/12/2015 11:46 PM Usage 1 (direct execution): java -server
-Xmx<memory> -jar <MHAP jar> -s<fasta/dat from/self file> [-q<fasta/dat to file>] [-f<kmer filter
list, must be sorted>] Usage 2 (generate precomputed binaries): java -server -Xmx<memory> -jar
<MHAP jar> -p<directory of fasta files> -q <output directory> [-f<kmer filter list, must be
sorted>]
--alignment, default = false
Experimental option.
--alignment-offset, default = -0.535
The offset to account for the variance in the alignment match score.
--alignment-score, default = 1.0E-6
The cutoff score for alignment matches.
--filter-threshold, default = 1.0E-5
[double], the cutoff at which the k-mer in the k-mer filter file is considered repetitive. This
value for a specific k-mer is specified in the second column in the filter file. If no filter file
is provided, this option is ignored.
--help, default = false
Displays the help menu.
--max-shift, default = 0.2
[double], region size to the left and right of the estimated overlap, as derived from the median
shift and sequence length, where a k-mer matches are still considered valid. Second stage filter
only.
--min-store-length, default = 0
[int], The minimum length of the read that is stored in the box. Used to filter out short reads
from FASTA file.
--nanopore-fast, default = false
Set all the parameters for the Nanopore fast settings. This is the current best guidance, and
could change at any time without warning.
--no-self, default = false
Do not compute the overlaps between sequences inside a box. Should be used when the to and from
sequences are coming from different files.
--num-hashes, default = 512
[int], number of min-mers to be used in MinHashing.
--num-min-matches, default = 3
[int], minimum # min-mer that must be shared before computing second stage filter. Any sequences
below that value are considered non-overlapping.
--num-threads, default = 12
[int], number of threads to use for computation. Typically set to 2 x #cores.
--pacbio-fast, default = false
Set all the parameters for the PacBio fast setting. This is the current best guidance, and could
change at any time without warning.
--pacbio-sensitive, default = false
Set all the parameters for the PacBio sensitive settings. This is the current best guidance, and
could change at any time without warning.
--store-full-id, default = false
Store full IDs as seen in FASTA file, rather than storing just the sequence position in the file.
Some FASTA files have long IDS, slowing output of results. This options is ignored when using
compressed file format.
--threshold, default = 0.04
[double], the threshold similarity score cutoff for the second stage sort-merge filter. This is
based on the average number of k-mers matching in the overlapping region.
--version, default = false
Displays the version and build time.
--weighted, default = false
Perform weighted MinHashing.
-f, default = ""
k-mer filter file used for filtering out highly repetative k-mers. Must be sorted in descending
order of frequency (second column).
-h, default = false
Displays the help menu.
-k, default = 16
[int], k-mer size used for MinHashing. The k-mer size for second stage filter is separate, and
cannot be modified.
-p, default = ""
Usage 2 only. The directory containing FASTA files that should be converted to binary format for
storage.
-q, default = ""
Usage 1: The FASTA file of reads, or a directory of files, that will be compared to the set of
reads in the box (see -s). Usage 2: The output directory for the binary formatted dat files.
-s, default = ""
Usage 1 only. The FASTA or binary dat file (see Usage 2) of reads that will be stored in a box,
and that all subsequent reads will be compared to.