ProDerAl: reference position dependent alignment

Benjamin Crysup; Bruce Budowle; August E Woerner

doi:10.1093/bioinformatics/btab008

ProDerAl: reference position dependent alignment

Bioinformatics. 2021 Aug 25;37(16):2479-2480. doi: 10.1093/bioinformatics/btab008.

Authors

Benjamin Crysup¹, Bruce Budowle¹, August E Woerner¹

Affiliation

¹ Center for Human Identification, University of North Texas, Fort Worth, TX 76107, USA.

PMID: 33459758
DOI: 10.1093/bioinformatics/btab008

Abstract

Motivation: Current read-mapping software uses a singular specification of alignment parameters with respect to the reference. In the presence of varying reference structures (such as the repetitive regions of the human genome), alignments can be improved if those parameters are allowed vary.

Results: To that end, the C++ program ProDerAl was written to refine previously generated alignments using varying parameters for these problematic regions. Synthetic benchmarks show that this realignment can result in an order of magnitude fewer misaligned bases.

Availability and implementation: *Nix users can retrieve the source from GitHub (https://github.com/Benjamin-Crysup/proderal.git). Windows binary available at https://github.com/Benjamin-Crysup/proderal/releases/download/v1.1/proderal.zip.

Supplementary information: Supplementary data are available at Bioinformatics online.

Abstract

Grants and funding