soapsnp command not found

Introduction

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

soapsnp: command not found

or when using sudo you get the following error message

sudo: soapsnp: command not found

Solutions to soapsnp: command not found

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

In Ubuntu soapsnp is provided by soapsnp package.

soapsnp is:

For getting ideas on the cause of diseases or their response to therapy, and for understanding either for a particular patient, doctors around the globe are starting to look at the genes or the whole genome and how that sequence is different from a healthy / well responding individual.

SOAPsnp is a member of the SOAP (Short Oligonucleotide Analysis Package). The program is a resequencing utility. It assembles the consensus sequence for the genome of a newly sequenced individual based on the alignment of the raw sequencing reads on a known reference. SNPs can then be identified on the consensus sequence through the comparison with the reference.

SOAPsnp uses a method based on Bayes’ theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors. All these kinds of information was integrated into a single quality score for each base in PHRED scale to measure the accuracy of consensus calling. Currently, it supports the alignment format of SOAPaligner (soap2).

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

sudo apt-get -y install soapsnp

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

You can also use apt command to install soapsnp.

sudo apt -y install soapsnp

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

sudo aptitude install soapsnp

Summary

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