GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis

Area of Science:

• Computational Biology
• Bioinformatics
• Genomics

Background:

• Pangenome analysis is crucial for understanding microbial evolution and function.
• Existing orthology-calling methods can be complex and inaccessible to non-bioinformaticians.
• There is a need for user-friendly tools for detailed pangenome and core genome analysis.

Purpose of the Study:

• To introduce GET_HOMOLOGUES, an open-source software package for accessible pangenome analysis.
• To provide customizable tools for clustering homologous gene families and analyzing microbial genomes.
• To facilitate comparative genomics, including the identification of lineage-specific genes and genome-wide comparisons.

Main Methods:

• Utilizes multiple orthology-calling algorithms: bidirectional best-hit, COGtriangles, and OrthoMCL.
• Incorporates adjustable stringency criteria including domain composition (HMMER3), alignment coverage, and synteny.
• Employs consensus clustering, auxiliary scripts for data interrogation and visualization, and mixture models for genome size estimation.

Main Results:

• GET_HOMOLOGUES enables customizable and detailed pangenome analyses for microorganisms.
• The software supports robust homologous gene family clustering through various algorithms and filtering options.
• It facilitates the generation of core genome and pangenome sets, estimation of genome sizes, and comparative genomics analyses.

Conclusions:

• GET_HOMOLOGUES democratizes advanced pangenome analysis for researchers, including non-bioinformaticians.
• The software's flexibility and efficiency, leveraging modern computing resources, make it a valuable tool for microbial genomics.
• It aids in understanding microbial diversity, evolution, and identifying key genetic elements through comprehensive pangenome studies.