Main menu

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 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.

Availability and implementation: https://github.com/lh3/minimap and https://github.com/lh3/miniasm

Authors: Heng Li

Getting started

Buy a MinION starter pack Nanopore store Sequencing service providers Channel partners

Nanopore technology

Subscribe to Nanopore updates Resources and publications What is the Nanopore Community

About Oxford Nanopore

News Company timeline Sustainability Leadership team Media resources & contacts For investors For partners Working at Oxford Nanopore Current vacancies Commercial information BSI 27001 accreditationBSI 90001 accreditationBSI mark of trust
Spanish flag