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

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*Is it possible to get the code used in this project?
 
*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).'''
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<br/>'''Pop, M. Genome assembly reborn: recent computational challenges. Briefings in Bioinformatics 10, 354-366 (2009).'''<br/>
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''Notes''
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''Thoughts''

Revision as of 14:41, 23 May 2011

June 16 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
  • 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