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

Revision as of 14:59, 23 May 2011

http://phagesdb.org/ - phage database. Assembled versions of the raw files we have are located here

http://www.cbcb.umd.edu/ - UMD bioinformatics center. Good open source programs. Also includes AMOS

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

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
- TOOL: Jellyfish - counts k-mers http://www.cbcb.umd.edu/software/jellyfish/
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).

Notes

Thoughts

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 == Useful Links ==
-http://phagesdb.org/
+http://phagesdb.org/ - phage database. Assembled versions of the raw files we have are located here
-http://www.cbcb.umd.edu/
+http://www.cbcb.umd.edu/ - UMD bioinformatics center. Good open source programs. Also includes AMOS
+http://seqanswers.com/forums/showthread.php?t=43 - a good list of assembly programs
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