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A mapper, minimap, and a de novo assembler, miniasm, for efficiently mapping and assembling single molecule real-time (SMRT) and Oxford Nanopore technologies (ONT) reads without an error correction stage. Miniasm implements the ‘O’ and ‘L’ steps in the overlap-layout consensus (OLC) assembly paradigm. It confirms long noisy reads can be assembled without an error correction stage, and without this stage, the assembly process can be greatly accelerated and simplified, while achieving comparable contiguity and large-scale accuracy to existing pipelines, at least for genomes without excessive repetitive sequences. 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, though the consensus sequence error rate is as high as raw reads.

Software type:
Toolkit
Interface:
Command line interface
Restrictions to use:
None
Biological technology:
Pacific Biosciences, Oxford Nanopore
Operating system:
Unix/Linux
License:
MIT License
Computer skills:
Advanced
Stability:
Stable
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Links

Additional informations

Minimap URL: https://github.com/lh3/minimap

Institution(s)

Broad Institute, Cambridge, MA, USA

Funding source(s)

NHGRI U54HG003037; NIH GM100233

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    PMID: 24930142
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    PMID: 21102452
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    PMID: 26944054

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