Motivation: Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10kbp 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 C. elegans data in 9 minutes, orders of magnitude faster than the existing pipelines. We also introduce a pairwise read mapping format (PAF) and a graphical fragment assembly format (GFA), and demonstrate the interoperability between ours and current tools.