Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
MOTIVATION 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. RESULTS 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. AVAILABILITY AND IMPLEMENTATION https:/github.com/lh3/minimap and https:/github.com/lh3/miniasm CONTACT hengli@broadinstitute.org SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Bioinform.