How To Install python3-nanoget on Kali Linux

In this tutorial we learn how to install python3-nanoget on Kali Linux. python3-nanoget is extract information from Oxford Nanopore sequencing data and alignments

Introduction

In this tutorial we learn how to install python3-nanoget on Kali Linux.

What is python3-nanoget

python3-nanoget is:

The Python3 module nanoget provides functions to extract useful metrics from Oxford Nanopore sequencing reads and alignments.

Data can be presented in the following formats, using the following functions:

  • sorted bam file process_bam(bamfile, threads)
  • standard fastq file process_fastq_plain(fastqfile, ’threads')
  • fastq file with metadata from MinKNOW or Albacore process_fastq_rich(fastqfile)
  • sequencing_summary file generated by Albacore process_summary(sequencing_summary.txt, ‘readtype’)

Fastq files can be compressed using gzip, bzip2 or bgzip. The data is returned as a pandas DataFrame with standardized headernames for convenient extraction. The functions perform logging while being called and extracting data.

There are three methods to install python3-nanoget 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 python3-nanoget Using apt-get

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

sudo apt-get update

After updating apt database, We can install python3-nanoget using apt-get by running the following command:

sudo apt-get -y install python3-nanoget

Install python3-nanoget Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install python3-nanoget using apt by running the following command:

sudo apt -y install python3-nanoget

Install python3-nanoget 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 python3-nanoget using aptitude by running the following command:

sudo aptitude -y install python3-nanoget

How To Uninstall python3-nanoget on Kali Linux

To uninstall only the python3-nanoget package we can use the following command:

sudo apt-get remove python3-nanoget

Uninstall python3-nanoget And Its Dependencies

To uninstall python3-nanoget and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove python3-nanoget

Remove python3-nanoget Configurations and Data

To remove python3-nanoget configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge python3-nanoget

Remove python3-nanoget configuration, data, and all of its dependencies

We can use the following command to remove python3-nanoget configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge python3-nanoget

Dependencies

python3-nanoget have the following dependencies:

References

Summary

In this tutorial we learn how to install python3-nanoget package on Kali Linux using different package management tools: apt, apt-get and aptitude.