Tuesday 21 August 2012

de novo assembly of 20 strains of Streptococcus mutans associated with severe tooth decay

http://nextgenseq.blogspot.sg/2012/08/i-gave-short-presentation-at-nyu-ctsi.html

(Stuart Brown) I gave a short presentation at the NYU CTSI Translational Research in Progress seminar this week about our sequencing work on strains of Streptococcus mutans associated with severe tooth decay in children.  We sequenced and did de novo assembly on each of 20 strains, then did an in silico subtraction to find unique genomic elements associated with health or disease.


Stuart Brown said...

ABySS gave us sets of contigs for each genome, from 20 to 300 contigs per genome. We used MAUVE as a sanity check- to see that the contigs align well with known genomes of the same species, and not miss any substantial chunk of the known genomes. Also makes a pretty figure for the presentation and paper. 

To link up the contigs into a single chromosome we would really need a large insert mate-pair library. A lot of work for 20 different strains. Not necessary for our approach.

the details are in this PDF file:

https://www.box.com/s/fbea9b1d5cdb96f07348

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