Connect with us

Software

OVarFlow- A GATK4-based variant calling workflow

Tariq Abdullah

Published

on

OVarFlow- A GATK4-based variant calling workflow

An automated workflow for single nucleotide polymorphisms detection is developed. This is known as OVarFlow [1]. This workflow also helps in the identification of insertions and deletions. 

OVarFlow provides a wide range of applications in sequence annotation of model and non-model organisms [1]. The workflow is based on GATK best practices. It makes the task of variant calling easy by reducing the computation time and resources.

A reference genome is provided as input in FASTA format along with reference annotation in a general feature format (.gff.gz). After that, second-generation sequencing data is provided in fastq format. Using this data, functionally annotated variants are generated. The workflow also consists of an extended workflow that generates variants by base quality score recalibration (BQSR).

OVarFlow is written in Python & Snakemake, and Bash languages and is available for Linux on GitLab.

For more information, read here.


References

  1. Bathke, J., Lühken, G. (2021). OVarFlow: a resource optimized GATK 4 based Open source Variant calling workFlow. BMC Bioinformatics 22, 402.

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

Advertisement
Click to comment

You must be logged in to post a comment Login

Leave a Reply

Software

[Tutorial] Installing Rosetta 3.21 on Ubuntu

Dr. Muniba Faiza

Published

on

Installing Rosetta on Ubuntu

Rosetta is a bioinformatics software for modeling and protein structure analysis [1]. In this article, we are going to install this software on Ubuntu. (more…)

Continue Reading

Software

Generating multiple low-energy conformers using Avogadro

Dr. Muniba Faiza

Published

on

Generating multiple low-energy conformers using Avogadro

In our previous article, we generated multiple conformers using OpenBabel. In this article, we are going to generate multiple low-energy conformers of a ligand using Avogadro [1]. (more…)

Continue Reading

Software

How to generate multiple conformers of a ligand using OpenBabel?

Dr. Muniba Faiza

Published

on

How to generate multiple conformers of a ligand using OpenBabel?

OpenBabel [1] offers several functions including file format conversion, generation of 3D structures from smiles, and so on. In this article, we are going to generate multiple conformers of a ligand using OpenBabel. (more…)

Continue Reading

LATEST ISSUE

ADVERT