Learning resources

Tutorials, workshops and seminars

To do bioinformatics well, you need to learn 3 things. The Unix shell (command line), a scripting language like Python (or Perl if you must), and the stats environment R. All are free, can be learnt online for free. Once you’ve learnt these things, you will be able to do pretty much anything in terms of bioinformatics analysis, including reading and parsing data files, analysing and plotting data, and making your own analysis pipelines.

Unix

• Unix
• Unix shell on Software Carpentry

Python

• Beginners: Non-programmer’s tutorial for Python by Josh Cogliati (PDF)
• Beginners: Python & programming trainig with Rosalind
• Beginners: Learn programming with Python (Coursera); check for new courses on Coursera too
• Some coding experience: Python tutorials from ANGUS
• Some coding experience: A primer on Python
• Some coding experience: Python intro talks on Software Carpentry (assumes basic programming concepts like variables, loops, conditionals, lists/arrays)
• Reference: PythonQuick – handy tutorial & reference for Python
• Reference: BioPython Tutorial – a Python package providing modules for common tasks in bioinformatics, including reading and writing sequence data
• Reference: BioPython wiki – examples on how to use some modules

Next Gen sequencing analysis

• ANGUS: Analyzing Next Gen Sequencing Data – Course by Titus Brown at Michigan State University, includes Unix, scripting R; read mapping, assembly, RNAseq, CHiPseq, SNP calling
• UTexas Bioinformatics wiki – includes mapping, variant calling, assembly, expression analysis and lots of other bits
• RNAseq course – course from the Netherlands Bioinformatics Centre (BioAssist)

Phylogenetics – also see software page

• Integrative Biology course at Berkeley – Phylogenetics & Evolution class, includes labs on Phylip, Mesquite, Paup, MrBayes, BEAST, r8s, R
• Evolution 101 at Berkeley – easy intro to concepts in evolution, including understanding and interpreting phylogenetic trees
• Bodega Phylogenetics course wiki – includes talks, papers and lab tutorials on all manner of phylogenetics analysis
• Phyloseminar.org – recorded seminars on phylo topics
• Divergence time estimation with BEAST – by Tracy Heath

Phylogenetics in R

• R in Ecology and Evolution – http://r-eco-evo.blogspot.com.au/
• R bloggers: Recology http://www.r-bloggers.com/author/recology-r/
• Talk introducing phylogenetics in R: http://www.r-bloggers.com/my-talk-on-doing-phylogenetics-in-r-2/
• Finding meaningful clusters in trees
• phytools blog, “Phylogenetic Tools for Comparative Biology”

Primers for people trained in computer science, maths or stats:

• Molecular Biology Primer – reading guide written by Daniel Choi, gives some useful pointers on reading the textbook Molecular Biology of the Cell (Alberts et al) available free (for searching but not browsing) at NCBI Bookshelf
• A Biology Primer For Computer Scientists – written by Franco Preparata for the Computational Molecular Biology course at Brown
• Developing effective bioinformatics programming skills
• Organizing computational biology projects

Papers & seminars introducing sequencing & next generation sequencing

• Primer on NGS, also see slides below

• Read alignment
• De novo assembly review 1, review 2, review 3, review 4.
• Applications to bacterial pathogens – Joseph & Read 2010, Pallen & Loman 2010

ECCB 2010 Next-gen sequencing Tutorial (Thomas Keane@Sanger)

Other slides from Thomas Keane

Bacterial genomics

• See this post of mine about bacterial populations and bacterial communities, and some of my work in this area
• Nature and dynamics of bacterial genomes

• Population structure, species concepts, horizontal transfer, homologous recombination
  • The pan-genome
  • Species concept
• Microevolution, subtyping, phylogeography
  • Towards the use of genomics to study microevolutionary change in bacteria
• Bacterial communities and metagenomics
  • Metagenomics primer
• See list of key papers and concepts

More Phylogenetics Methods

• Phylogeny for the faint of heart (Sandra Baldauf, 2003, Trends in Genetics)
• Phylogenetic Analyses: A Toolbox Expanding towards Bayesian Methods (Aris-Brosou & Xia, 2008, Int J Plant Genomics)
• Phylogenetics course @ Berkeley
• Article on phylogenomics (Philippe et al, 2011, PLoS Biology). Includes an explanation of phylogenomics, and glossary of terms relating to phylogenetics & phylogenomics.
• 2011 Bodega workshop – Phylogenetics wiki. Lecture slides and tutorials from a workshop in March 2011. Covers software packages like MrBayes, RAxML, R, BEAST, BayesTraits and topics including model selection, divergence dating, discrete & continuous character evolution, diversification rates.
• PLoS Currents – Tree of Life
• Phyloseminar.Org – online seminars in phylogenetics!

Useful sources of information

• Databases: NCBI, EBI
• Forums: SEQanswers, BioStar
• Talks: SlideShare – Jon Eisen
• Bioinformatics (journal) – Next gen sequencing virtual issue
• Briefings in Bioinformatics (journal) – Second generation sequencing issue (Sep 2010)
• PLoS:
  • Ten Simple Rules – series of articles with tips for grad students, getting published, presenting
  • Genomics of Emerging Infectious Disease (PLoS Collections)
• NCBI Bookshelfof online books, e.g.:
  • Comparative Genomics: Sequence – Evolution – Function
  • Medical Microbiology
  • Genomes (note, published in 2002 i.e. pre-NGS and many of the more recent genomes, but still a good source for the basics)
  • Intro to genetic analysis (not browsable)