«
»

Looking for genome assembly papers

I’m starting a journal club for the computer scientists at BiRC.  Since it is me starting it up, I have egoistically chosen a subject I personally would like to learn more about.  Algorithms for Next Generation Sequencing assembly.

Now I don’t even know much about the “plain old” sequence assembly algorithms, so I want to start out with a few papers on that and then move to newer algorithms.

The only problem is that I don’t know which papers are important and which are not.

So if anyone have any ideas, please please let me know!

–

33-54=-21

Tags: , ,

This entry was posted on Monday, February 2nd, 2009 at 8:56 pm and is filed under Work. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site.

6 Responses to “Looking for genome assembly papers”

  1. Frank Says:
    February 3rd, 2009 at 3:20 am

    Here are a couple of papers on de novo (or comparative genome) assembly that you may be interested.

    ALLPATHS: De novo assembly of whole-genome shotgun microreads
    Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
    A new pheromone trail-based genetic algorithm for comparative genome assembly
    OSLay: optimal syntenic layout of unfinished assemblies

  2. Thomas Mailund Says:
    February 3rd, 2009 at 8:11 am

    Thanks Frank!

  3. Animesh Sharma| Says:
    February 3rd, 2009 at 7:38 pm

    I did some compilation of links last year, http://www.ii.uib.no/~animesh/ . A bit old but covers most of the tools for basic assembly :)

  4. Thomas Mailund Says:
    February 3rd, 2009 at 7:46 pm

    Thanks, that will come in handy!

  5. Jonathan Says:
    February 4th, 2009 at 11:17 pm

    Heng Li, author of MAQ, has a good listing of short read assembly papers/algorithms.

    http://www.sanger.ac.uk/Users/lh3/seq-nt.html

  6. Thomas Mailund Says:
    February 5th, 2009 at 7:44 am

    Thanks Jonathan!

Leave a Reply