title: Correcting base-assignment errors in repeat regions of shotgun assembly.
abstract: Accurate base-assignment in repeat regions of a whole genome shotgun assembly is an unsolved problem. Since reads in repeat regions cannot be easily attributed to a unique location in the genome, current assemblers may place these reads arbitrarily. As a result, the base-assignment error rate in repeats is likely to be much higher than that in the rest of the genome. We developed an iterative algorithm, EULER-AIR, that is able to correct base-assignment errors in finished genome sequences in public databases. The Wolbachia genome is among the best finished genomes. Using this genome project as an example, we demonstrated that EULER-AIR can 1) discover and correct base-assignment errors, 2) provide accurate read assignments, 3) utilize finishing reads for accurate base-assignment, and 4) provide guidance for designing finishing experiments. In the genome of Wolbachia, EULER-AIR found 16 positions with ambiguous base-assignment and two positions with erroneous bases. Besides Wolbachia, many other genome sequencing projects have significantly fewer finishing reads and, hence, are likely to contain more base-assignment errors in repeats. We demonstrate that EULER-AIR is a software tool that can be used to find and correct base-assignment errors in a genome assembly project.
authors.affiliation: Bioinformatics Program, University of California, San Diego, La Jolla 92093, USA. dzhi@ucsd.edu
authors.forename: Degui
authors.initials: D
authors.lastname: Zhi
authors.forename: Uri
authors.initials: U
authors.lastname: Keich
authors.forename: Pavel
authors.initials: P
authors.lastname: Pevzner
authors.forename: Steffen
authors.initials: S
authors.lastname: Heber
authors.forename: Haixu
authors.initials: H
authors.lastname: Tang
mesh_terms: D000465:Algorithms; D016123:Campylobacter jejuni / Q000235:genetics; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D016680:Genome, Bacterial; D013294:Lactococcus lactis / Q000235:genetics; D015233:Models, Statistical; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000706:statistics & numerical data; D012984:Software; D013212:Staphylococcus epidermidis / Q000235:genetics; D020577:Wolbachia / Q000235:genetics