Biology Faculty Articles

Title

HalSynteny: A fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments

Document Type

Article

Publication Date

6-10-2020

Publication Title

GigaScience

Keywords

comparative genomics, genome alignments, HAL format, Synteny blocks

ISSN

2047217X

Volume

9

Issue/No.

6

Abstract

Background: Large-scale sequencing projects provide high-quality full-genome data that can be used for reconstruction of chromosomal exchanges and rearrangements that disrupt conserved syntenic blocks. The highest resolution of cross-species homology can be obtained on the basis of whole-genome, reference-free alignments. Very large multiple alignments of full-genome sequence stored in a binary format demand an accurate and efficient computational approach for synteny block production. Findings: halSynteny performs efficient processing of pairwise alignment blocks for any pair of genomes in the alignment. The tool is part of the HAL comparative genomics suite and is targeted to build synteny blocks for multi-hundred-way, reference-free vertebrate alignments built with the Cactus system. Conclusions: halSynteny enables an accurate and rapid identification of synteny in multiple full-genome alignments. The method is implemented in C++11 as a component of the halTools software and released under MIT license. The package is available at https://github.com/ComparativeGenomicsToolkit/hal/.

DOI

10.1093/gigascience/giaa047

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