Error correction and assembly complexity of single molecule sequencing reads
Citations Over Time
Abstract
Abstract 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.
Related Papers
- → Assisted assembly: how to improve a de novo genome assembly by using related species(2009)70 cited
- → Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study(2011)54 cited
- → GAGE: A critical evaluation of genome assemblies and assembly algorithms(2011)747 cited
- → Efficient algorithms for sequence assembly(2013)
- Assisted assembly: how to improve a de novo genome assembly by using related species(2009)