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  • De novo fragment assembly with short mate-paired reads, Does the read length matter?

    Increasing read length is currently viewed as the crucial condition for fragment assembly with next-generation sequencing technologies. However, introducing mate-paired reads (separated by a gap of length, GapLength) opens a possibility to transform short mate-pairs into long mate-reads of length ap …


    Genome Res. 2009 Jan 13. [Epub ahead of print]

    De novo fragment assembly with short mate-paired reads: Does the read length matter?

    Chaisson MJ, Brinza D, Pevzner PA.

    Increasing read length is currently viewed as the crucial condition for fragment assembly with next-generation sequencing technologies. However, introducing mate-paired reads (separated by a gap of length, GapLength) opens a possibility to transform short mate-pairs into long mate-reads of length approximately GapLength, and thus raises the question as to whether the read length (as opposed to GapLength) even matters. We describe a new tool, EULER-USR, for assembling mate-paired short reads and use it to analyze the question of whether the read length matters. We further complement the ongoing experimental efforts to maximize read length by a new computational approach for increasing the effective read length. While the common practice is to trim the error-prone tails of the reads, we present an approach that substitutes trimming with error correction using repeat graphs. An important and counterintuitive implication of this result is that one may extend sequencing reactions that degrade with length "past their prime" to where the error rate grows above what is normally acceptable for fragment assembly.

  • #2
    Hello,

    I just read this paper and I'm a bit puzzled on where to get the EULER-USR version. The paper sends you here. On the posts there you can find links to the EULER-SR tarball, which I guess is the previous version. I've tried registering, but didn't get any confirmation email.

    My guess is that the site is no longer being updated. Actually, the last post there was on 03/30/2009

    Any tips on how/where to get EULER-USR would be greatly appreciated

    Greetings,
    Leonardo
    L. Collado Torres, Ph.D. student in Biostatistics.

    Comment


    • #3
      I believe EULER-SR version 1.1.2 is the last version.

      Comment


      • #4
        I think that EULER-SR and EULER-USR are different versions. Am I wrong?
        L. Collado Torres, Ph.D. student in Biostatistics.

        Comment

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