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

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ID: 292361
2016
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Abstract
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 Contact: hengli@broadinstitute.org
Reference Key
openalex_W2194172909 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Heng Li
Journal BMC Bioinformatics
Year 2016
DOI
10.1093/bioinformatics/btw152
URL
https://academic.oup.com/bioinformatics/article-pdf/32/14/2103/19567911/btw152.pdf
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