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minimap website  

Minimap is an experimental tool to efficiently find multiple approximate mapping positions between two sets of long sequences, such as between reads and reference genomes, between genomes and between long noisy reads. By default, it is tuned to have high sensitivity to 2kb matches around 20% divergence but with low specificity. Minimap does not generate alignments as of now and because of this, it is usually tens of times faster than mainstream aligners. With four CPU cores, minimap can map 1.6Gbp PacBio reads to human in 2.5 minutes, 1Gbp PacBio E. coli reads to pre-indexed 9.6Gbp bacterial genomes in 3 minutes, to pre-indexed >100Gbp nt database in ~1 hour (of which ~20 minutes are spent on loading index from the network filesystem; peak RAM: 10GB), map 2800 bacteria to themselves in 1 hour, and map 1Gbp E. coli reads against themselves in a couple of minutes.

Required Modules


  • minimap

System Variables

  • HPC_MINIMAP_DIR - installation directory
  • HPC_MINIMAP_BIN - executable directory
  • HPC_MINIMAP_DOC - documentation directory