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© Research
Publication : iScience

Mapping-friendly sequence reductions: Going beyond homopolymer compression.

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in iScience - 18 Nov 2022

Blassel L, Medvedev P, Chikhi R,

Link to Pubmed [PMID] – 36339268

Link to DOI – 10.1016/j.isci.2022.105305

iScience 2022 Nov; 25(11): 105305

Sequencing errors continue to pose algorithmic challenges to methods working with sequencing data. One of the simplest and most prevalent techniques for ameliorating the detrimental effects of homopolymer expansion/contraction errors present in long reads is homopolymer compression. It collapses runs of repeated nucleotides, to remove some sequencing errors and improve mapping sensitivity. Though our intuitive understanding justifies why homopolymer compression works, it in no way implies that it is the best transformation that can be done. In this paper, we explore if there are transformations that can be applied in the same pre-processing manner as homopolymer compression that would achieve better alignment sensitivity. We introduce a more general framework than homopolymer compression, called mapping-friendly sequence reductions. We transform the reference and the reads using these reductions and then apply an alignment algorithm. We demonstrate that some mapping-friendly sequence reductions lead to improved mapping accuracy, outperforming homopolymer compression.

https://pubmed.ncbi.nlm.nih.gov/36339268