How To Install sortmerna on Kali Linux

In this tutorial we learn how to install sortmerna on Kali Linux. sortmerna is tool for filtering, mapping and OTU-picking NGS reads

Introduction

In this tutorial we learn how to install sortmerna on Kali Linux.

What is sortmerna

sortmerna is:

SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. The core algorithm is based on approximate seeds and allows for fast and sensitive analyses of nucleotide sequences. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. Additional applications include OTU-picking and taxonomy assignation available through QIIME v1.9+ (http://qiime.org - v1.9.0-rc1). SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart rRNA and rejected reads into two files specified by the user. Optionally, it can provide high quality local alignments of rRNA reads against the rRNA database. SortMeRNA works with Illumina, 454, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments.

There are three methods to install sortmerna on Kali Linux. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install sortmerna Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install sortmerna using apt-get by running the following command:

sudo apt-get -y install sortmerna

Install sortmerna Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install sortmerna using apt by running the following command:

sudo apt -y install sortmerna

Install sortmerna Using aptitude

If you want to follow this method, you might need to install aptitude on Kali Linux first since aptitude is usually not installed by default on Kali Linux. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install sortmerna using aptitude by running the following command:

sudo aptitude -y install sortmerna

How To Uninstall sortmerna on Kali Linux

To uninstall only the sortmerna package we can use the following command:

sudo apt-get remove sortmerna

Uninstall sortmerna And Its Dependencies

To uninstall sortmerna and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove sortmerna

Remove sortmerna Configurations and Data

To remove sortmerna configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge sortmerna

Remove sortmerna configuration, data, and all of its dependencies

We can use the following command to remove sortmerna configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge sortmerna

Dependencies

sortmerna have the following dependencies:

References

Summary

In this tutorial we learn how to install sortmerna package on Kali Linux using different package management tools: apt, apt-get and aptitude.