View source for Genome Assembly Project: Leland Taylor '12

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'''Kingsford, C., Schatz, M.C. & Pop, M. Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics 11, 21 (2010).'''<br/><br/>

''Notes''
*Use De Brujin graphs to estimate "completeness" of genomes assembled via ''de novo'' assembly
**Find Eulerian path(s) in these graphs
**Note the assumptions made in the paper
*Lists compression techniques and the order to employ them
*Can use this method to compute N50
**N50 = the length of the largest contig (m) such that at least 50% of genome covered by contigs of size >= m. 
**A higher N50 score usually correlates to a more "correct" genome
*Regardless of correctness of genome, for nearly all read sizes (1000nt > size > 25nt), 85%+ of genes accurately identified (85% is for 25nt reads).

''Thoughts''
*Look for assembler that uses De Brujin graph?
*This paper showed how to get an upper limit of correctness of genome. Compare several existing ''de novo'' assemblers using the methods here as comparison. 
*Is it possible to get the code used in this project?

'''Pop, M. Genome assembly reborn: recent computational challenges. Briefings in Bioinformatics 10, 354-366 (2009).'''