Topic outline

  • General

    Doctoral Program in Population Genomics SIB PhD Training Network

    Joint Summer School
    SIB PhD Training Network and Doctoral Program in Population Genomics

    Bioinformatics and Population Genomics

    Adelboden, 17-22 June 2012


    Hotel Hari, Adelboden


    detailed program here

    If you aren't very familiar with UNIX and/or R, please try to brush up your skills before coming.

    List of tools (that have to be installed in your laptops before the course)
    Test that everything works before the course.

    - Terminal and SHH
    - Mac and Linux computers should have these already.
    - Windows: Install PuTTY (simple) or Cygwin (advanced; install X11 for X window support)
    - FTP
    - Any OS: FileZilla
    - Mac: Cyberduck
    - Windows: WinSCP
    - R
    - Optional but useful - Perl for Windows (Mac and Linux have Perl & Ruby already)
    - Java
    - Cytoscape version 2.8 (requires Java)
    - Fastqc (requires Java)
    - Genome viewers
    - IGV (requires Java; choose the 1.2GB version)
    - Apollo

    Laptops minimum requirements
    Any relatively recent machine will be OK with either Linux, Mac or Windows. (If your laptop is more than 5 years old then (a) respect! and (b) email us and we'll look into that)

    Preliminary Reading

    1. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011). Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics 12, 499-510.
    2. The Heliconius Genome Consortium (2012). Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature (Advance Online Publication) Full text (Open Access) | PDF | Supplementary information | doi:10.1038/nature11041
    3. Gadau J, Helmkampf M, Nygaard S, Roux J, Simola DF, Smith CR, Suen G, Wurm Y, Smith CD (2012) The genomic impact of 100 million years of social evolution in seven ant species. Trends in Genetics - 1 January 2012 (Vol. 28, Issue 1, pp. 14-21)
    4. Garber, M., et al. (2011) Computational methods for transcriptome annotation and quantification using RNA-seq, Nat Methods, 8, 469-477.
    5. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28(5), 511-15.