---
name: "minimap2.py"
section: "1"
platform: "linux"
package: "python3-mappy"
version: "2.27+dfsg-1+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/minimap2.py"
---

# minimap2.py(1)

minimap2 Python3 interface

## NAME

minimap2.py - minimap2 Python3 interface

## SYNOPSIS

**minimap2.py** \[*options*\] *\<ref.fa\>\|\<ref.mmi\> \<query.fq\>*

## OPTIONS

- **-x** STR

  preset: sr, map-pb, map-ont, asm5, asm10 or splice

- **-n** INT

  mininum number of minimizers

- **-m** INT

  mininum chaining score

- **-k** INT

  k-mer length

- **-w** INT

  minimizer window length

- **-r** INT

  band width

- **-c**

  output the cs tag

## AUTHOR

 This manpage was written by Andreas Tille for the Debian distribution and\
  can be used for any other usage of the program.