bbmap.sh command not found

Introduction

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

bbmap.sh: command not found

or when using sudo you get the following error message

sudo: bbmap.sh: command not found

Solutions to bbmap.sh: command not found

How To Fix bbmap.sh: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu bbmap.sh is provided by bbmap package.

bbmap is:

The BBTools are a collection of small programs to solve recurrent tasks for the creative handling of short biological RNA/DNA sequences. This suite may be best known for its mapper, which is also the name of the project on sourceforge, but several tools have been added over time. All tools are multi-threaded, implemented platform-independently in Java:

BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant of errors and numerous large indels.

BBNorm: Kmer-based error-correction and normalization tool.

Dedupe: Simplifies assemblies by removing duplicate or contained subsequences that share a target percent identity.

Reformat: Reformats reads between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over 500 MB/s.

BBDuk: Filters, trims, or masks reads with kmer matches to an artifact/contaminant file.

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

sudo apt-get -y install bbmap

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

You can also use apt command to install bbmap.

sudo apt -y install bbmap

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

sudo aptitude install bbmap

Summary

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