Genome Assembly Lab Meeting

Wednesday 6/13/2007, noon, 425 HMMB (see Lab Meeting)

• Salzberg et al review (Mitch):
  • Genome Sequence Assembly - Algorithms and Issues. http://lcbb1.epfl.ch/compbio07/sequencing.pdf

• Batzoglou/Arachne (Rob):
  • Batzoglou et al.: ARACHNE: a whole-genome shotgun assembler. Genome Res. 2002;12:177-89.

• Myers (Avinash):
  • Myers &: The fragment assembly string graph. Bioinformatics 2005;21 Suppl 2:ii79-85.

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Followup ideas & further reading...

Ian's list

• Myers
  • Myers &: The fragment assembly string graph. Bioinformatics 2005;21 Suppl 2:ii79-85.
  • Myers et al.: On the sequencing and assembly of the human genome. Proc. Natl. Acad. Sci. U.S.A. 2002;99:4145-6.
  • Huson et al.: Design of a compartmentalized shotgun assembler for the human genome. Bioinformatics 2001;17 Suppl 1:S132-9.
  • Myers et al.: A whole-genome assembly of Drosophila. Science 2000;287:2196-204.
• Pevzner
  • Pevzner et al.: De novo repeat classification and fragment assembly. Genome Res. 2004;14:1786-96.
  • Chaisson et al.: Fragment assembly with short reads. Bioinformatics 2004;20:2067-74.
  • Pevzner et al.: An Eulerian path approach to DNA fragment assembly. Proc. Natl. Acad. Sci. U.S.A. 2001;98:9748-53.
  • Zhi et al.: Correcting base-assignment errors in repeat regions of shotgun assembly. IEEE/ACM Trans Comput Biol Bioinform 2007;4:54-64.
  • ...?

Avinash's List

• Review:
  • Genome Sequence Assembly - Algorithms and Issues. http://lcbb1.epfl.ch/compbio07/sequencing.pdf

• Overlap-Layout-Consensus approach:
  • Combinatorial Algorithms for DNA sequence assembly. http://www.springerlink.com/content/m222gl7q72240386/ (A very long paper).
  • Batzoglou et al.: ARACHNE: a whole-genome shotgun assembler. Genome Res. 2002;12:177-89.

• Eulerian Path Approach.
  • Pevzner et al.: An Eulerian path approach to DNA fragment assembly. Proc. Natl. Acad. Sci. U.S.A. 2001;98:9748-53.
  • Fragment assembly with double-barreled data. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/suppl_1/S225

• Problems due to repeats.
  • Separating repeats in DNA sequence assembly. http://portal.acm.org/citation.cfm?id=369192&dl=ACM&coll=portal