Advertisement
Research Article

Whole-Genome Sequencing and Assembly with High-Throughput, Short-Read Technologies

  • Andreas Sundquist mail,

    To whom correspondence should be addressed. E-mail: asundqui@cs.stanford.edu

    Affiliation: Department of Computer Science, Stanford University, Stanford, California, United States of America

    X
  • Mostafa Ronaghi,

    Affiliation: Stanford Genome Technology Center, Stanford, California, United States of America

    X
  • Haixu Tang,

    Affiliation: School of Informatics, Indiana University, Bloomington, Indiana, United States of America

    X
  • Pavel Pevzner,

    Affiliation: Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, United States of America

    X
  • Serafim Batzoglou

    Affiliation: Department of Computer Science, Stanford University, Stanford, California, United States of America

    X
  • Published: May 30, 2007
  • DOI: 10.1371/journal.pone.0000484

Reader Comments (6)

Post a new comment on this article

Operations Research for Strategic Genomics

Posted by jaredroach on 07 Jun 2007 at 18:26 GMT

I think this is a great article that adds to the armamentarium of strategies for sequencing genomes. The most successful strategies will be those that add information without adding (much) cost. The authors present a strategy that uses binning to add this information. The authors recognize that binning (as they envision it) is currently fairly expensive. However, it is important for readers and reviewers of papers in strategic genomics to welcome papers that anticipate technology. Anticipatory papers can shape a better future. Waiting to analyze and publish strategies after the fact may be interesting, but may end up playing more of a role of historical footnote.

Pairwise end-sequencing also was criticized in the early 1990s because of the additional cost (both of increased molecular biology + handling + tracking clones as well as decreased read lengths compared to m13 sequencing). However, as we began to understand the informational advantages of pairing the reads, increased efforts at improving the implementation may have been driven in part by this understanding, and so theory and technology advanced hand-in-hand. This may also happen for the proposed strategy.

I note the authors use the concept of “ideal” on at least one occasion. One anonymous reviewer once rejected this word from my prose on the grounds that determination of “ideal” (similarly to “optimal”) requires analysis of all conceivable strategies. Maybe that has not been done here either… …perhaps go with “very good.”