Near-optimal assembly for shotgun sequencing with noisy reads

BMC Bioinformatics. 2014;15 Suppl 9(Suppl 9):S4. doi: 10.1186/1471-2105-15-S9-S4. Epub 2014 Sep 10.


Recent work identified the fundamental limits on the information requirements in terms of read length and coverage depth required for successful de novo genome reconstruction from shotgun sequencing data, based on the idealistic assumption of no errors in the reads (noiseless reads). In this work, we show that even when there is noise in the reads, one can successfully reconstruct with information requirements close to the noiseless fundamental limit. A new assembly algorithm, X-phased Multibridging, is designed based on a probabilistic model of the genome. It is shown through analysis to perform well on the model, and through simulations to perform well on real genomes.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Base Sequence
  • Computer Simulation
  • Escherichia coli / genetics
  • Genome*
  • Genomics / methods*
  • Models, Genetic
  • Probability
  • Repetitive Sequences, Nucleic Acid
  • Sequence Analysis, DNA / methods*
  • Signal-To-Noise Ratio