ProDerAl: reference position dependent alignment.
basic_science · Level V
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- Record sourced from PubMed, PMID 33459758.
- Also identified by DOI 10.1093/bioinformatics/btab008.
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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. 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. *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 data are available at Bioinformatics online.