---
name: "mhap"
section: "1"
platform: "linux"
package: "mhap"
version: "2.1.3+dfsg-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/mhap"
---

# mhap(1)

probabilistic sequence overlapping

## NAME

mhap - probabilistic sequence overlapping

## SYNOPSIS

**mhap** **-s**\<fasta/dat from/self file\> \[-q\<fasta/dat to file\>\] \[-f\<kmer filter list, must be sorted\>\]\
 **java** **-server** **-Xmx**\<memory\> **-jar** $(which mhap) **-s**\<fasta/dat from/self file\> \[-q\<fasta/dat to file\>\] \[-f\<kmer filter list, must be sorted\>\]\
 generate precomputed binaries:\
 **java** **-server** **-Xmx**\<memory\> **-jar** $(which mhap) **-p**\<directory of fasta files\> **-q** \<output directory\> \[-f\<kmer filter list, must be sorted\>\]

## DESCRIPTION

MHAP (MinHash Alignment Protocol) is a tool for finding overlaps of long-read sequences (such as PacBio or Nanopore) in bioinformatics.

## OPTIONS

- **-h --help**

  Show summary of available options.

- **--version**

  Displays the version.