Minimap2: pairwise alignment for nucleotide sequences

By Heng Li. Bioinform., 2017

13,069 citations recorded by the source corpus.

Motivation Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms. Results Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥100 bp in length, ≥1 kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions and introduces new heuristics to reduce spurious alignments. It is 3-4 times as fast as mainstream short-read mappers at comparable accuracy, and is ≥30 times faster than long-read genomic or cDNA mappers at higher accuracy, surpassing most aligners specialized in one type of alignment. Availability and implementation https://github.com/lh3/minimap2. Supplementary information Supplementary data are available at Bioinformatics online.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a47483dca56d93dabc54c8d49a5d03c6fb1e9771

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In Molecular Biology

Citations in the corpus

CoverM: read alignment statistics for metagenomics (2025, positive): “Next, the reads are aligned to the reference sequences using Strobealign (Sahlin 2022), Minimap2 (Li 2018), or BWA (Li 2013).”
Assignment of Epidemiological Lineages in an Emerging Pandemic Using the Pangolin Tool (2021, neutral): “17 (Li 2018).”
Major impacts of widespread structural variation on gene expression and crop improvement in tomato (2020, positive): “Contigs were mapped to both references with Minimap2 (-k19 -w19) (Li, 2018).”
Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing (2021, positive): “RagTag supports the use of Minimap2, Unimap, or Nucmer for whole-genome alignment, though any alignments in PAF or MUMmer’s delta format can be used [23,24].”
SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline (2018, methodology): “The software Bowtie2 (Langmead and Salzberg, 2012) is used for this task, but we also included Minimap2 (Li, 2018) for the mapping of long MinION reads.”