ASGART: fast and parallel genome scale segmental duplications mapping.

Motivation: Segmental Duplications (SDs) are DNA fragments longer than 1 kbp, distributed within and between chromosomes and sharing more than 90% identity. Although they hold a significant role in genomic fluidity and adaptability, many key questions about their intrinsic characteristics and mutability remain unsolved due to the persistent difficulty of sequencing highly duplicated genomic regions. The recent development of long and linked-read NGS technologies will increase the need to search for SDs in genomes newly sequenced with these technics. The main limitation of SD analysis will soon be the availability of efficient detection software, to retrieve and compare SD genomic component between species or lineages.

Results: In this paper, we present the open-source ASGART, 'A Segmental duplications Gathering And Refining Tool', developed to search for segmental duplications (SDs) in any assembled sequence. We have tested and benchmarked ASGART on five models organisms. Our results demonstrate ASGART's ability to extract SDs from any genome-wide sequence, regardless of genomic size or organizational complexity and quicker than any other software available.

Availability and implementation: The online version of ASGART is available at https://asgart.irit.fr. The source code of ASGART is available both on the ASGART website and at https://github.com/delehef/asgart.

Supplementary information: Supplementary data are available at Bioinformatics online.