Minimap and miniasm | Datasets2Tools

General Information

Description	Fast mapping and de novo assembly for noisy long sequences
Homepage	https://github.com/lh3/minimap

Publications

Bioinformatics (2016)

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

Heng Li

Motivation: Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10 kb 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 Caenorhabditis elegans data in 9 min, orders of magnitude faster than the existing pipelines, though the consensus sequence error rate is as high as raw reads. We also introduce a pairwise read mapping format and a graphical fragment assembly format, 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

Supplementary information: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btw152

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