How To Install racon on Kali Linux
Introduction
In this tutorial we learn how to install racon on Kali Linux.
What is racon
racon is:
Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.
Racon can be used as a polishing tool after the assembly with either Illumina data or data produced by third generation of sequencing. The type of data inputed is automatically detected.
Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ format and overlaps/alignments between the reads and the contigs in MHAP/PAF/SAM format. Output is a set of polished contigs in FASTA format printed to stdout. All input files can be compressed with gzip.
Racon can also be used as a read error-correction tool. In this scenario, the MHAP/PAF/SAM file needs to contain pairwise overlaps between reads including dual overlaps.
A wrapper script is also available to enable easier usage to the end- user for large datasets. It has the same interface as racon but adds two additional features from the outside. Sequences can be subsampled to decrease the total execution time (accuracy might be lower) while target sequences can be split into smaller chunks and run sequentially to decrease memory consumption. Both features can be run at the same time as well.
There are three methods to install racon 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 racon Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get updateAfter updating apt database, We can install racon using apt-get by running the following command:
sudo apt-get -y install raconInstall racon Using apt
Update apt database with apt using the following command.
sudo apt updateAfter updating apt database, We can install racon using apt by running the following command:
sudo apt -y install raconInstall racon 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 updateAfter updating apt database, We can install racon using aptitude by running the following command:
sudo aptitude -y install raconHow To Uninstall racon on Kali Linux
To uninstall only the racon package we can use the following command:
sudo apt-get remove raconUninstall racon And Its Dependencies
To uninstall racon and its dependencies that are no longer needed by Kali Linux, we can use the command below:
sudo apt-get -y autoremove raconRemove racon Configurations and Data
To remove racon configuration and data from Kali Linux we can use the following command:
sudo apt-get -y purge raconRemove racon configuration, data, and all of its dependencies
We can use the following command to remove racon configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge raconDependencies
racon have the following dependencies:
References
Summary
In this tutorial we learn how to install racon package on Kali Linux using different package management tools: apt, apt-get and aptitude.