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Correcting Base-Assignment Errors in Repeat Regions of Shotgun Assembly
January-March 2007 (vol. 4 no. 1)
pp. 54-64
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.
Index Terms:
Fragment assembly, finishing, expectation maximization.
Citation:
Degui Zhi, Uri Keich, Pavel Pevzner, Steffen Heber, Haixu Tang, "Correcting Base-Assignment Errors in Repeat Regions of Shotgun Assembly," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 4, no. 1, pp. 54-64, Jan.-March 2007, doi:10.1109/TCBB.2007.1005
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