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.

mhap 1.6                                         September 2015                                          MHAP(1)