minimap2 command not found

Introduction

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

minimap2: command not found

or when using sudo you get the following error message

sudo: minimap2: command not found

Solutions to minimap2: command not found

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

In Ubuntu minimap2 is provided by minimap2 package.

minimap2 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%.

For ~10kb noisy reads sequences, minimap2 is tens of times faster than mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It is more accurate on simulated long reads and produces biologically meaningful alignment ready for downstream analyses. For >100bp Illumina short reads, minimap2 is three times as fast as BWA-MEM and Bowtie2, and as accurate on simulated data. Detailed evaluations are available from the minimap2 paper or the preprint.

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

sudo apt-get -y install minimap2

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

You can also use apt command to install minimap2.

sudo apt -y install minimap2

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

sudo aptitude install minimap2

Summary

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