minimap2
versatile pairwise aligner for genomic and spliced nucleotide sequences
Install
- All systems
-
curl cmd.cat/minimap2.sh
- Debian
-
apt-get install minimap2
- Ubuntu
-
apt-get install minimap2
- Kali Linux
-
apt-get install minimap2
- Windows (WSL2)
-
sudo apt-get update
sudo apt-get install minimap2
- Dockerfile
- dockerfile.run/minimap2
minimap2
versatile 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 reads against 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%. For ~10kb noisy reads sequences, minimap2 is tens of times faster than mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It is more accurate on simulated long reads and produces biologically meaningful alignment ready for downstream analyses. For >100bp Illumina short reads, minimap2 is three times as fast as BWA-MEM and Bowtie2, and as accurate on simulated data. Detailed evaluations are available from the minimap2 paper or the preprint.