How To Install python3-sqt on Ubuntu

Posted on April 1, 2023 (Last modified on May 20, 2023 )

3 minutes • 561 words

Introduction

In this tutorial we learn how to install python3-sqt on Ubuntu.

What is `python3-sqt`

python3-sqt is:

sqt is a collection of command-line tools for working with high-throughput sequencing data. Conceptionally not fixed to use any particular language, many sqt subcommands are currently implemented in Python. For them, a Python package is available with functions for reading and writing FASTA/FASTQ files, computing alignments, quality trimming, etc.

The following tools are offered:

sqt-coverage – Compute per-reference statistics such as coverage and GC content
sqt-fastqmod – FASTQ modifications: shorten, subset, reverse complement, quality trimming.
sqt-fastastats – Compute N50, min/max length, GC content etc. of a FASTA file
sqt-qualityguess – Guess quality encoding of one or more FASTA files.
sqt-globalalign – Compute a global or semiglobal alignment of two strings.
sqt-chars – Count length of the first word given on the command line.
sqt-sam-cscq – Add the CS and CQ tags to a SAM file with colorspace reads.
sqt-fastamutate – Add substitutions and indels to sequences in a FASTA file.
sqt-fastaextract – Efficiently extract one or more regions from an indexed FASTA file.
sqt-translate – Replace characters in FASTA files (like the ’tr' command).
sqt-sam-fixn – Replace all non-ACGT characters within reads in a SAM file.
sqt-sam-insertsize – Mean and standard deviation of paired-end insert sizes.
sqt-sam-set-op – Set operations (union, intersection, …) on SAM/BAM files.
sqt-bam-eof – Check for the End-Of-File marker in compressed BAM files.
sqt-checkfastqpe – Check whether two FASTQ files contain correctly paired paired-end data.

There are three methods to install python3-sqt on Ubuntu. 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-sqt 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-sqt using apt-get by running the following command:

sudo apt-get -y install python3-sqt

Install python3-sqt Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install python3-sqt

Install python3-sqt Using aptitude

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

sudo aptitude update

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

sudo aptitude -y install python3-sqt

How To Uninstall python3-sqt on Ubuntu

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

sudo apt-get remove python3-sqt

Uninstall python3-sqt And Its Dependencies

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

sudo apt-get -y autoremove python3-sqt

Remove python3-sqt Configurations and Data

To remove python3-sqt configuration and data from Ubuntu we can use the following command:

sudo apt-get -y purge python3-sqt

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

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

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

Dependencies

python3-sqt have the following dependencies:

References

python3-sqt website

Summary

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