G-Anchor: a novel approach for whole-genome comparative mapping utilising evolutionary conserved DNA sequences

Lenis, V E and Swain, M and Larkin, D M (2018) G-Anchor: a novel approach for whole-genome comparative mapping utilising evolutionary conserved DNA sequences. GigaScience, 7 (5).

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Abstract

Here we introduce G-Anchor, a new, fast, and efficient pipeline that uses a strictly limited but highly effective set of local sequence alignments to anchor (or map) an animal genome to another species’ reference genome. G-Anchor makes novel use of a databank of highly conserved DNA sequence elements. We demonstrate how these elements may be aligned to a pair of genomes, creating anchors. These anchors enable the rapid mapping of scaffolds from a de novo assembled genome to chromosome assemblies of a reference species. Our results demonstrate that G-Anchor can successfully anchor a vertebrate genome onto a phylogenetically related reference species genome using a desktop or laptop computer within a few hours, and with comparable accuracy to that achieved by a highly accurate whole-genome alignment tool such as LASTZ. G-Anchor thus makes whole-genome comparisons accessible to researchers with limited computational resources.