preparing for the workshop

The Workshop is an intensive course taught at a high level and fast pace, and thus provides no opportunities for concurrent preparation and reading. Therefore, it is most helpful to prepare for the Workshop ahead of time. Among the specific steps useful in preparing for the Workshop include the following.

  • Do background reading in appropriate areas-see the reading lists for each Workshop, below. This web site provides you with information regarding the material covered. You should review this information to determine areas in which you require more study before attending the Workshop.
  • Become comfortable with UNIX-based operating systems. At minimum you will need to know how to log on to a system, move, copy, and delete files, change directories, and use a text editor. Check out the UNIX tutorial for more information.
  • Put together an example data set relevant to your research. Although there will be example data sets provided for the computer demonstrations, having a data set with which you are familiar will be of help. Having the data edited and assembled will help ensure your time is spent productively and in such a way as to take advantage of the special resources available at the Workshop.
  • Lecture notes and associated materials for many of the lectures and demonstrations will be put on the web site as they become available. Materials from previous Workshops are available on the schedule page.


Workshop on Molecular Evolution: Suggested Reading

Fundamentals of Molecular Evolution (Graur and Li 2000)
Molecular Evolution (Li 1997)
Molecular Evolutionary Genetics (Nei 1987)
The phylogenetic inference chapter in Molecular Systematics (Swofford et al. 1996)
Molecular Evolution: A Phylogenetic Approach (Page and Holmes 1998)
Two review papers, authored by Paul Lewis and Mark Holder (Lewis 2001, Holder and Lewis 2003)

Workshop on Comparative Genomics: Suggested Reading


Modern Genome Sequencing Technology
A decade's perspective on DNA sequencing technology
Next-generation DNA sequencing methods
The impact of next-generation sequencing technology on genetics
Field guide to next-generation DNA sequencers


Genome Structure Variation
Genome structural variation discovery and genotyping
Mapping copy number variation by population-scale genome sequencing


Transcriptomics
Computational methods for transcriptome annotation and quantification using RNA-seq
Computation for ChIP-seq and RNA-seq studies
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Genome-wide mapping of in vivo protein-DNA interactions


Assembly
De novo transcriptome assembly with ABySS
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
Aligning short sequencing reads with Bowtie.


Galaxy
Integrating diverse databases into an unified analysis framework: a Galaxy approach
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.


GMOD/Gbrowse
The generic genome browser: a building block for a model organism system database
Getting Started with GMOD


Metagenomics
A Primer on Metagenomics
QIIME allows analysis of high-throughput community sequencing data
Supervised classification of human microbiota
The Metagenomics RAST server
MEGAN analysis of metagenomic data


Programming
Getting Started with BioPerl
PyCogent: a toolkit for making sense from sequence