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Motivation: Single Molecule Real-Time (SMRT) sequencing technology and OxfordNanopore technologies (ONT) produce reads over 10kbp in length, which haveenabled high-quality genome assembly at an affordable cost. However, atpresent, long reads have an error rate as high as 10-15%. Complex andcomputationally 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 errorcorrection stage. They can often assemble a sequencing run of bacterial datainto a single contig in a few minutes, and assemble 45-fold C. elegans data in9 minutes, orders of magnitude faster than the existing pipelines. We alsointroduce a pairwise read mapping format (PAF) and a graphical fragmentassembly format (GFA), and demonstrate the interoperability between ours andcurrent tools.  Availability and implementation: https://github.com/lh3/minimap andhttps://github.com/lh3/miniasm  Contact: hengli@broadinstitute.org

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences