Singletrack: An Algorithm for Improving Memory Consumption and Performance of Gap-Affine Sequence Alignment

Lorién López‐Villellas

doi:10.1093/bioinformatics/btag183

Singletrack: An Algorithm for Improving Memory Consumption and Performance of Gap-Affine Sequence Alignment

2026-04-13

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L

Lorién López‐Villellas *

C

Cristian Iñiguez

A

Albert Jiménez-Blanco

Jesús Alastruey-Benedé

DOI：10.1093/bioinformatics/btag183

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Abstract

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Advances in DNA sequencing have outpaced advances in computation, making sequence alignment a major bottleneck in genome data analyses. Classical dynamic programming (DP) algorithms are particularly memory-intensive, especially when computing gap-affine and dual gap-affine alignments. Existing strategies to reduce memory consumption often sacrifice speed or alignment accuracy.

Keywords:

Sequence alignment

Gap-affine

Memory consumption

Dynamic programming

DNA sequencing

Singletrack: An Algorithm for Improving Memory Consumption and Performance of Gap-Affine Sequence Alignment

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