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Updated: Feb 21, 2026
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G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
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Accelerating minimap2 for whole-genome alignment
Ghanshyam Chandra1, Md Vasimuddin2, Sanchit Misra2
1Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, KA 560012, India.
Bioinformatics (Oxford, England)
|February 19, 2026
Summary
New whole-genome alignment software, mm2-plus, improves efficiency for long-read sequencing data. It accelerates alignment by optimizing CPU use, leading to faster results without sacrificing accuracy.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Long-read sequencing generates large, chromosome-spanning DNA sequences.
- Current whole-genome alignment tools struggle with parallelization efficiency due to fewer, longer sequences, leading to underutilized CPUs and increased runtimes.
Purpose of the Study:
- To develop a faster and more efficient whole-genome alignment method for long-read sequencing data.
- To address the suboptimal CPU utilization and longer runtimes of existing alignment tools.
Main Methods:
- Developed mm2-plus, an enhanced version of the minimap2 aligner.
- Implemented a fine-grained parallel chaining algorithm.
- Introduced a rapid method for distinguishing primary and secondary alignment chains.
Main Results:
- Achieved significant acceleration in whole-genome alignment for human, plant, and primate genomes.
- Observed speedups ranging from 1.6× to 7.2×.
- Maintained alignment accuracy comparable to existing methods.
Conclusions:
- mm2-plus offers a substantial improvement in speed and efficiency for whole-genome alignment of long-read sequencing data.
- The optimizations effectively address the challenges posed by large, contiguous genomic sequences.
- This advancement is crucial for accelerating genomic analysis pipelines.
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