Genome Assembly Project: Leland Taylor '12

Useful Links

http://phagesdb.org/ http://www.cbcb.umd.edu/

November 21 2024

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