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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 ONTdoi:10.1093/bioinformatics/btw152 pmid:27153593 pmcid:PMC4937194 fatcat:lde73lu5ozaq7k2544l4x3npoa