ArticleJournal of biotechnology and biomedicine2023
Accelerating Minimap2 for Accurate Long Read Alignment on GPUs.
Article in Journal of biotechnology and biomedicine, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Article
- WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology.PLoS computational biology · 2026Article
- Accelerating minimap2 for whole-genome alignment.Bioinformatics (Oxford, England) · 2026Article
- Col-BWT: Pangenomic Seed Chaining with Maximal Matches Improves Read Classification.Journal of computational biology : a journal of computational molecular cell biology · 2026Article
- Pilot study: a descriptive-retrospective analysis of SARS-CoV-2 variants distribution and phylogenesis in the Phlegraean area.Frontiers in molecular biosciences · 2025Article
- Article
- Improved pangenomic classification accuracy with chain statistics.bioRxiv : the preprint server for biology · 2024Article
- Rapid brain lymphoma diagnostics through nanopore sequencing of cytology-negative cerebrospinal fluid.Acta neuropathologica · 2024Article
- Article
- Efficient end-to-end long-read sequence mapping using minimap2-fpga integrated with hardware accelerated chaining.Scientific reports · 2023Article
- The Progression in Developing Genomic Resources for Crop Improvement.Life (Basel, Switzerland) · 2023Review
- Efficient mapping of accurate long reads in minimizer space with mapquik.Genome research · 2023Article
- BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis.NAR genomics and bioinformatics · 2023Article
- From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures.Computational and structural biotechnology journal · 2022Review
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Authors and funding
6 authors.
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Abstract
Long read sequencing technology is becoming increasingly popular for Precision Medicine applications like Whole Genome Sequencing (WGS) and microbial abundance estimation. Minimap2 is the state-of-the-art aligner and mapper used by the leading long read sequencing technologies, today. However, Minimap2 on CPUs is very slow for long noisy reads. ~60-70% of the run-time on a CPU comes from the highly sequential chaining step in Minimap2. On the other hand, most Point-of-Care computational workflows in long read sequencing use Graphics Processing Units (GPUs). We present minimap2-accelerated (mm2-ax), a heterogeneous design for sequence mapping and alignment where minimap2's compute intensive chaining step is sped up on the GPU and demonstrate its time and cost benefits. We extract better intra-read parallelism from chaining without losing mapping accuracy by forward transforming Minimap2's chaining algorithm. Moreover, we better utilize the high memory available on modern cloud instances apart from better workload balancing, data locality and minimal branch divergence on the GPU. We show mm2-ax on an NVIDIA A100 GPU improves the chaining step with 5.41 - 2.57X speedup and 4.07 - 1.93X speedup : costup over the fastest version of Minimap2, mm2-fast, benchmarked on a Google Cloud Platform instance of 30 SIMD cores.
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Registered trials
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