minimap2.py command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

minimap2.py: command not found

or when using sudo you get the following error message

sudo: minimap2.py: command not found

Solutions to minimap2.py: command not found

How To Fix minimap2.py: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu minimap2.py is provided by python3-mappy package.

python3-mappy is:

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Typical use cases include: (1) mapping PacBio or Oxford Nanopore genomic reads to the human genome; (2) finding overlaps between long reads with error rate up to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA reads against a reference genome; (4) aligning Illumina single- or paired-end reads; (5) assembly-to-assembly alignment; (6) full- genome alignment between two closely related species with divergence below ~15%.

This package contains the Python3 interface for using minimap2.

To fix this problem, we can install more using the command below.

sudo apt-get -y install python3-mappy

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install python3-mappy.

sudo apt -y install python3-mappy

Or if you have aptitude installed you can use the following command.

sudo aptitude install python3-mappy

Summary

In this tutorial we learn how to fix minimap2.py command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.