pbindex command not found

Introduction

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

pbindex: command not found

or when using sudo you get the following error message

sudo: pbindex: command not found

Solutions to pbindex: command not found

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

In Ubuntu pbindex is provided by pbbamtools package.

pbbamtools is:

The BAM format is a binary, compressed, record-oriented container format for raw or aligned sequence reads. The associated SAM format is a text representation of the same data. The specifications for BAM/SAM are maintained by the SAM/BAM Format Specification Working Group.

PacBio-produced BAM files are fully compatible with the BAM specification, but makes use of the extensibility mechanisms of the BAM specification to encode PacBio-specific information.

This package provides command-line utilities for working with PacBio BAM files.

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

sudo apt-get -y install pbbamtools

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

You can also use apt command to install pbbamtools.

sudo apt -y install pbbamtools

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

sudo aptitude install pbbamtools

Summary

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