title: Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction.
abstract: BACKGROUND
  With the rapid expansion of DNA sequencing databases, it is now feasible to identify relevant information from prior sequencing projects and completed genomes and apply it to de novo sequencing of new organisms. As an example, this paper demonstrates how such extra information can be used to improve de novo assemblies by augmenting the overlapping step. Finding all pairs of overlapping reads is a key task in many genome assemblers, and to this end, highly efficient algorithms have been developed to find alignments in large collections of sequences. It is well known that due to repeated sequences, many aligned pairs of reads nevertheless do not overlap. But no overlapping algorithm to date takes a rigorous approach to separating aligned but non-overlapping read pairs from true overlaps.
  
  
  RESULTS
  We present an approach that extends the Minimus assembler by a data driven step to classify overlaps as true or false prior to contig construction. We trained several different classification models within the Weka framework using various statistics derived from overlaps of reads available from prior sequencing projects. These statistics included percent mismatch and k-mer frequencies within the overlaps as well as a comparative genomics score derived from mapping reads to multiple reference genomes. We show that in real whole-genome sequencing data from the E. coli and S. aureus genomes, by providing a curated set of overlaps to the contigging phase of the assembler, we nearly doubled the median contig length (N50) without sacrificing coverage of the genome or increasing the number of mis-assemblies.
  
  
  CONCLUSIONS
  Machine learning methods that use comparative and non-comparative features to classify overlaps as true or false can be used to improve the quality of a sequence assembly.
authors.affiliation: Siemens Corporate Research, 755 College Road East, Princeton, NJ, USA. lance.palmer@siemens.com
authors.forename: Lance E
authors.initials: LE
authors.lastname: Palmer
authors.forename: Mathaeus
authors.initials: M
authors.lastname: Dejori
authors.forename: Randall
authors.initials: R
authors.lastname: Bolanos
authors.forename: Daniel
authors.initials: D
authors.lastname: Fasulo
mesh_terms: D001185:Artificial Intelligence; D001483:Base Sequence; D030561:Databases, Nucleic Acid; D016680:Genome, Bacterial; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*