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ProDerAl: reference position dependent alignment

NCJ Number
302958
Journal
Bioinformatics Volume: 37 Issue: 16 Dated: August 2021 Pages: 2479–2480
Date Published
August 2021
Length
2 pages
Author(s)
Benjamin Crysup; Bruce Budowle; August E Woerner
Agencies
NIJ-Sponsored
Annotation

This article considers the rationale for and the availability of the C++ program ProDerAl, which was written to refine previously generated alignments using varying parameters for these problematic regions, and synthetic benchmarks show that this realignment can result in an order of magnitude fewer misaligned bases.

Abstract

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. 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. (publisher abstract modified)

Date Created: November 1, 2021