Error correction and assembly complexity of single molecule sequencing reads
Hayan Lee*, James Gurtowski*, Shinjae Yoo, Shoshana Marcus, W. Richard McCombie, and Michael Schatz
Third generation single molecule sequencing technology is poised to revolutionize genomics by
enabling the sequencing of long, individual molecules of DNA and RNA. These technologies now
routinely produce reads exceeding 5,000 basepairs, and can achieve reads as long as 50,000 basepairs.
Here we evaluate the limits of single molecule sequencing by assessing the impact of long read
sequencing in the assembly of the human genome and 25 other important genomes across the tree
of life. From this, we develop a new data-driven model using support vector regression that
can accurately predict assembly performance. We also present a novel hybrid error correction
algorithm for long PacBio sequencing reads that uses pre-assembled Illumina sequences for
the error correction. We apply it several prokaryotic and eukaryotic genomes, and show it
can achieve near-perfect assemblies of small genomes (<100Mbp) and substantially improved
assemblies of larger ones. All source code and the assembly model are available open-source.
E. coli
S. cerevisiae W303
A. thaliana Ler-0
O. sativa Nipponbare
O. sativa IR64
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