title: Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.
abstract: Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10 kb in length, which have enabled high-quality genome assembly at an affordable cost. However, at present, long reads have an error rate as high as 10-15%. Complex and computationally intensive pipelines are required to assemble such reads.
  
  
  
  We present a new mapper, minimap and a de novo assembler, miniasm, for efficiently mapping and assembling SMRT and ONT reads without an error correction stage. They can often assemble a sequencing run of bacterial data into a single contig in a few minutes, and assemble 45-fold Caenorhabditis elegans data in 9 min, orders of magnitude faster than the existing pipelines, though the consensus sequence error rate is as high as raw reads. We also introduce a pairwise read mapping format and a graphical fragment assembly format, and demonstrate the interoperability between ours and current tools.
  
  
  
  https://github.com/lh3/minimap and https://github.com/lh3/miniasm
  
  
  
  hengli@broadinstitute.org
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Medical Population Genetics, Broad Institute, Cambridge, MA 02142, USA.
authors.forename: Heng
authors.initials: H
authors.lastname: Li
mesh_terms: D000818:Animals; D001419:Bacteria / Q000235:genetics; D017173:Caenorhabditis elegans / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D017422:Sequence Analysis, DNA; D012984:Software