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.