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NGSEP 4: Efficient and accurate identification of orthogroups and whole‐genome alignment

2022; Wiley; Volume: 23; Issue: 3 Linguagem: Inglês

10.1111/1755-0998.13737

1755-0998

Daniel Tello, Laura González, Jorge M. Gómez, Juan Camilo Zuluaga‐Monares, Rogelio Garcia, Ricardo Angel, Daniel Mahecha, Erick Duarte, Maria del Rosario Leon, Fernando Reyes, Camilo Escobar‐Velásquez, Mario Linares‐Vásquez, Nicolás Cardozo, Jorge Duitama,

Chromosomal and Genetic Variations

Whole-genome alignment allows researchers to understand the genomic structure and variation among genomes. Approaches based on direct pairwise comparisons of DNA sequences require large computational capacities. As a consequence, pipelines combining tools for orthologous gene identification and synteny have been developed. In this manuscript, we present the latest functionalities implemented in NGSEP 4, to identify orthogroups and perform whole genome alignments. NGSEP implements functionalities for identification of clusters of homologus genes, synteny analysis and whole genome alignment. Our results showed that the NGSEP algorithm for orthogroups identification has competitive accuracy and efficiency in comparison to commonly used tools. The implementation also includes a visualization of the whole genome alignment based on synteny of the orthogroups that were identified, and a reconstruction of the pangenome based on frequencies of the orthogroups among the genomes. NGSEP 4 also includes a new graphical user interface based on the JavaFX technology. We expect that these new developments will be very useful for several studies in evolutionary biology and population genomics.