Singletrack: an algorithm for improving memory consumption and performance of gap-affine sequence alignment

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.

We present Singletrack, an efficient algorithm for backtrace gap-affine and dual gap-affine alignments that requires storing a single DP matrix while preserving optimal alignment results. Compared to classical DP algorithms, Singletrack removes the need to store additional matrices (i.e. 2 for gap-affine and 4 for dual gap-affine), significantly reducing memory consumption and, in turn, reducing pressure on the memory hierarchy and improving overall performance. Most importantly, Singletrack is a general backtrace method compatible with state-of-the-art DP-based algorithms and heuristics, such as the Suzuki-Kasahara (SK) and the Wavefront Alignment (WFA) algorithms. We demonstrate that Singletrack reduces memory consumption for both SK and WFA algorithms, lowering SK usage by 2× and 4× and WFA usage by 3× and 5× for gap-affine and dual gap-affine alignments, respectively. Moreover, replacing KSW2's memory-reduction technique with Singletrack accelerates its SK implementation by up to 1.4× at the cost of doubling memory consumption, while Singletrack increases the performance of the WFA implementation in WFA2-lib by 1.2-2.1×. Compared to the efficient linear-memory BiWFA algorithm, the Singletrack-accelerated version of WFA trades a practical increase in memory usage for up to 5.2× higher performance.

The Singletrack implementations presented in this work are available on Zenodo (DOI: 10.5281/zenodo.18770585) and GitHub (https://github.com/LorienLV/singletrack).