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Minimap2

Jul 20, 2023

Pairwise aligner for genomic and spliced nucleotide sequences

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Typical use cases include 1 mapping PacBio or Oxford Nanopore genomic reads to the human genome 2 finding overlaps between long reads with error rate up to ~15 3 splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA readsagainst a reference genome 4 aligning Illumina single- or paired-end reads 5 assembly-to-assembly alignment 6 full-genome alignment between two closely related species with divergence below ~15

Checkout these related ports:
  • Wise - Intelligent algorithms for DNA searches
  • Wfa2-lib - Exact gap-affine algorithm using homology to accelerate alignment
  • Vt - Discovers short variants from Next Generation Sequencing data
  • Vsearch - Versatile open-source tool for metagenomics
  • Viennarna - Alignment tools for the structural analysis of RNA
  • Velvet - Sequence assembler for very short reads
  • Vcftools - Tools for working with VCF genomics files
  • Vcflib - C++ library and CLI tools for parsing and manipulating VCF files
  • Vcf2hap - Generate .hap file from VCF for haplohseq
  • Vcf-split - Split a multi-sample VCF into single-sample VCFs
  • Unikmer - Toolkit for nucleic acid k-mer analysis, set operations on k-mers
  • Unanimity - Pacific Biosciences consensus library and applications
  • Ugene - Integrated bioinformatics toolkit
  • Ucsc-userapps - Command line tools from the UCSC Genome Browser project
  • Trimmomatic - Flexible read trimming tool for Illumina NGS data