RT Journal Article
SR Electronic
T1 Error correction and assembly complexity of single molecule sequencing reads
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 006395
DO 10.1101/006395
A1 Hayan Lee
A1 James Gurtowski
A1 Shinjae Yoo
A1 Shoshana Marcus
A1 W. Richard McCombie
A1 Michael Schatz
YR 2014
UL http://biorxiv.org/content/early/2014/06/18/006395.abstract
AB 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.Abbreviationsbpbase pairGbpgigabasesMbpmegabasesSNPsingle nucleotide polymorphism