How To Install mosdepth on Kali Linux

In this tutorial we learn how to install mosdepth on Kali Linux. mosdepth is BAM/CRAM depth calculation biological sequencing

Introduction

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

What is mosdepth

mosdepth is:

Many small reads are produced by high-throughput “next generation” sequencing technologies. The final sequence is derived from how these reads are overlapping towards a consensus. The more reads are covering/confirming parts of a nucleotide seq, the higher the confidence is. Too many reads would be indicative of e.g. repeats in the genome.

mosdepth can output:

  • per-base depth about 2x as fast samtools depth–about 25 minutes of CPU time for a 30X genome.
  • mean per-window depth given a window size–as would be used for CNV calling.
  • the mean per-region given a BED file of regions.
  • a distribution of proportion of bases covered at or above a given threshold for each chromosome and genome-wide.
  • quantized output that merges adjacent bases as long as they fall in the same coverage bins e.g. (10-20)
  • threshold output to indicate how many bases in each region are covered at the given thresholds. when appropriate, the output files are bgzipped and indexed for ease of use.

There are three methods to install mosdepth 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 mosdepth Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install mosdepth

Install mosdepth Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install mosdepth

Install mosdepth 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 mosdepth using aptitude by running the following command:

sudo aptitude -y install mosdepth

How To Uninstall mosdepth on Kali Linux

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

sudo apt-get remove mosdepth

Uninstall mosdepth And Its Dependencies

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

sudo apt-get -y autoremove mosdepth

Remove mosdepth Configurations and Data

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

sudo apt-get -y purge mosdepth

Remove mosdepth configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge mosdepth

Dependencies

mosdepth have the following dependencies:

References

Summary

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