soap command not found

In this troubleshooting guide we learn how to fix soap command not found error message

Introduction

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

soap: command not found

or when using sudo you get the following error message

sudo: soap: command not found

Solutions to soap: command not found

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

In Ubuntu soap is provided by soapaligner package.

soapaligner is:

This package addresses a common problem in bioinformatics that has become routine now also in clinical research: the assembly and comparison of the very long genomic DNA sequences from many short reads that the machines provide.

SOAPaligner/soap2 is a member of the Short Oligonucleotide Analysis Package (SOAP) and an updated version of SOAP software for short oligonucleotide alignment (soap v1). The new program features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer. Compared to soap v1, it is one order of magnitude faster. It require only 2 minutes aligning one million single-end reads onto the human reference genome. Another remarkable improvement of SOAPaligner is that it now supports a wide range of the read length.

SOAPaligner/soap2 benefitted in time and space efficiency by a revolution in the basic data structures and algorithms used. The core algorithms and the indexing data structures (2way-BWT) are developed by the algorithms research group of the Department of Computer Science, the University of Hong Kong (T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu).

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

sudo apt-get -y install soapaligner

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

You can also use apt command to install soapaligner.

sudo apt -y install soapaligner

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

sudo aptitude install soapaligner

Summary

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