CSB1000 - Special topics in Genomics: the Hazelnut Blight Genome Project

Organized by David Guttman and Alan Moses

• 'Next generation' sequencing technology
• Animations explaining sequencing methods in this Wellcome Trust news story
  
• Reviews: Mardis Trends in Genetics 2008, Maclean et al. Nat. Rev. Microbiology 2009, Shendure & Ji Nat. Biotech 2008.
• More about Hazelnut Blight
• a P avellanae fact sheet
• Evolution of Hazelnut pathogens: Wang et al. Microbiology 2007
• Lecutre slides from Oct. 14th
  
• Short read assembly (reading for Oct. 21st)
  
• Review of genome assembly and short read assembly: Pop Briefings in Bioinformatics 2009
  
• Short read assembly with Velvet: Zerbino & Birney Genome Research 2008
  
• Short read assembly of mate paired reads (with error correction): Chaisson & Pevzner Genome Research 2009
• A very recent technical article on de novo assembly from Illumina (Solexa)
• Sequenced pseudomonas genomes Pph 1448A, PtoDC3000, Psy B728a
• Genome Annotation (reading for Nov. 18th)
• Background reviews. Genefinding: Brent & Guigó Curr Opin Struct Biol. 2004, Hology assignments: Koonin, E.V., Annu Rev Genet 2005, Functional annotation: Friedberg I. Brief Bioinform. 2006
• The GLIMMER gene-finder: Delcher et al. Nucleic Acids Res. 1999
• TIGRfam database: Haft et al. Nucleic Acids Res. 2001
• Automated annotation pipeline:  BMC Genomics.Aziz et al. 2008
  

• The course schedule can be found here.
• Some commands for servers are listed here.
• From a windows based computer, you can use putty to log in to the server and winSCP to transfer files
• The instructions for the final project