2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2017
Abstrakt

Heng Li. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics, 32(14):2103-2110. 2016.

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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:
hengli@broadinstitute.org SUPPLEMENTARY INFORMATION: Supplementary data are
available at Bioinformatics online.