I thought I would knock together a quick post listing a few useful introductory papers that I have sent to people on multiple occasions, just to save a bit of time. I will also include any suggestions that other people use to introduce others to the rapidly expanding world of bacterial genomic epidemiology. EDIT: going a bit meta here, but another great page of recommendations for getting started is from the Hanage Lab at CCDD, available here.

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Bioinformatics/Coding

http://www.homolog.us/blogs/blog/2011/07/22/a-beginners-guide-to-bioinformatics-part-i/

A Quick Guide to Organizing Computational Biology Projects

Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data

TOOLS FOR BACTERIAL COMPARATIVE GENOMICS (this, and above, from Kat Holt)

Another nice blog by Kat Holt on microbial genomics methods.

Coursera bioinformatics specialisation. Good general intro.

Code academy, learn the command line. Good for beginners as all you need is a web browser!

Learn python the hard way – by far the best free online python course.

Once you are a bit more advanced, you might want to try your skills on some of the rosalind problems. There is one set focussed on algorithms and one set focussed on tools.

Schatz lab resources – amazing python notebooks on fundamental topics and some practical tips on tools to use.

Bacterial genomics and epidemiology

Advantages of WGS for national (USA) surveillance of Listeria

Revolutionising Public Health Reference Microbiology using Whole Genome Sequencing: Salmonella as an exemplar

Twenty Years of Bacterial Genome Sequencing, Loman & Pallen, 2015

Bacterial genomes in epidemiology—present and future, Croucher et al., 2013

Evolution of MRSA During Hospital Transmission and Intercontinental Spread, Harris et al., 2010

Insights from Genomics into Bacterial Pathogen Populations, Wilson, 2013

Trees for the faint of heart, Baldauf, 2003

How to read a phylogenetic tree, Andy Rambaut

http://public-health-genomics.phe.org.uk/

An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella

Some great slides by @jennifergardy on the more practical aspects of genomic epidemiology

A VERY comprehensive report on Putting Pathogen Genomics into Practice by the PHG foundation.

More good stuff from Gardy about genomic epi in outbreak situations.

Genome assembly and annotation

http://pathogenomics.bham.ac.uk/blog/2009/09/tips-for-de-novo-bacterial-genome-assembly/

http://www.nature.com/nbt/journal/v29/n11/full/nbt.2023.html

http://bib.oxfordjournals.org/content/early/2012/03/08/bib.bbs007.full Fragment assembly with short reads, Chaisson, 2004

Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data, Edwards, 2013

 http://www.cs.jhu.edu/~langmea/resources/lecture_notes/assembly_dbg.pdf

RNA-seq

General background

http://rnaseq.uoregon.edu/

http://rnajournal.cshlp.org/content/early/2016/03/30/rna.053959.115.abstract

https://github.com/griffithlab/rnaseq_tutorial/wiki

Transcript quantification/differential gene expression

HiSat-stringtie-ballgown – http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html

Salmon – http://salmon.readthedocs.io/en/latest/salmon.html

Kallisto + sleuth https://pachterlab.github.io/kallisto/about http://pachterlab.github.io/sleuth/about.html

Alpine – http://www.nature.com/nbt/journal/v34/n12/full/nbt.3682.html

Assembly/splice variant analysis

http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html

http://biorxiv.org/content/early/2016/11/20/088765

http://hibberdlab.com/transrate/