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

ABSTRACT:

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

[e-mail]

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Li H 

PROVIDER: S-EPMC4937194 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature