Difference between revisions of "Genome Assembly Project: Leland Taylor '12"

Revision as of 14:24, 23 May 2011

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

Use De Brujin graphs to estimate "completeness" of genomes
- 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).

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

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 == {{CURRENTMONTHNAME}} {{CURRENTDAY}} {{CURRENTYEAR}} ==
-#Kingsford, C., Schatz, M.C. & Pop, M. Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics 11, 21 (2010).
+'''Kingsford, C., Schatz, M.C. & Pop, M. Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics 11, 21 (2010).'''
 *Use De Brujin graphs to estimate "completeness" of genomes
 **Find Eulerian path(s) in these graphs
@@ Line 10: / Line 10: @@
 *Regardless of correctness of genome, for nearly all read sizes (1000nt > size > 25nt), 85%+ of genes accurately identified (85% is for 25nt reads).
-#Pop, M. Genome assembly reborn: recent computational challenges. Briefings in Bioinformatics 10, 354-366 (2009).
+'''Pop, M. Genome assembly reborn: recent computational challenges. Briefings in Bioinformatics 10, 354-366 (2009).'''