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Genome Annotation and Assembly

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GAAP: A GUI-based Genome Assembly and Annotation Package.

Deepak Singla¹, Inderjit Singh Yadav¹

¹School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.

Current Genomics

|February 13, 2023

Summary

This summary is machine-generated.

Genome Assembly and Annotation software (GAAP) provides a free, user-friendly solution for analyzing next-generation sequencing data. This platform-independent tool automates genome assembly and gene prediction, addressing a gap in current bioinformatics software.

Keywords:

GUI NGS annotation gene prediction genome assembly software

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Area of Science:

Bioinformatics
Genomics
Computational Biology

Background:

Next-generation sequencing (NGS) generates vast amounts of data requiring efficient analysis tools.
Existing GUI-based software for NGS data analysis is often commercial, creating accessibility barriers.
There is a need for freely available, integrated software for comprehensive genome analysis.

Purpose of the Study:

To develop a user-friendly, platform-independent software for genome assembly and annotation.
To provide an integrated solution for the entire NGS data analysis pipeline.
To address the gap in accessible bioinformatics tools for researchers.

Main Methods:

Developed Genome Assembly and Annotation software (GAAP) using NodeJS, HTML, and JavaScript.
Integrated tools for quality control (FastQC, Trimmomatic), genome assembly (Velvet), and gene prediction (Prodigal).
Utilized remote NCBI Blast and IPR-Scan for gene annotation, with PERL and JavaScript for backend processing.

Main Results:

GAAP successfully assembled and annotated viral, bacterial, and human genomes.
A COVID-19 genome was assembled into a single contig with high reference coverage, predicting 11 genes.
Bacterial and human genomes were assembled with significant contig numbers and N50 values.

Conclusions:

GAAP is a freely available, comprehensive software package for genome assembly and annotation.
The software offers a complete data analysis solution, including quality checks, assembly, and annotation.
GAAP facilitates accessible and efficient analysis of NGS data for diverse genomic applications.