An article published in GenomeBiology presents Strobealign: a novel and fast method to compute seeds based on syncmers and strobemers for candidate location detection in sequence mapping applications.
We also ran the alignment tools with 4, 8, and 16 threads on the different datasets from the SIM3 dataset. Alignment time nearly halves for the tools when doubling the number of threads suggesting that the tools utilized the resources well . Relative alignment times between the tools for 4 and 8 threads stay similar to our benchmarks using 16 threads.
For our single-end data experiments , we largely observe the same results reported for the paired-end evaluation. Strobealign is the fastest tool for all read lengths of 150 nt and above. Although strobealign has slightly worse performance on high-diversity datasets in single-end mode , it has substantially higher accuracy and percentage of aligned reads to the tools with similar speed . Minimap2 performs well for the single-end reads of the highest diversity .
In summary, for the hg38 paired-end read analysis, strobealign has the best tradeoff between accuracy, runtime, and percent aligned reads to any of the other benchmarked aligners on most of the datasets. Strobealign and BWA-MEM have the highest accuracies across diversity levels for reads of lengths 150nt and above and are usually within a difference of 0.1% to each other.
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