Microbial Bioinformatics starter kit

by Lauren Cowley
You’re new to Bioinformatics and have no idea where to start. Let me suggest you give these tutorials/helpages a go:

  • https://c2-d2.github.io/hanage-lab/Bioinformatics-for-bacterial-population-genomics/
  • https://learnpythonthehardway.org
  • http://epidemic.bio.ed.ac.uk/how_to_read_a_phylogeny
  • https://angus.readthedocs.io/en/2017/
  • https://norwegianveterinaryinstitute.github.io/BioinfTraining/
  • https://bitsandbugs.org/2017/06/26/salmonella-genomic-epidemiology-exercise/
  • https://bitsandbugs.org/2016/09/22/guideline-to-bioinformatics-tools/
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The Amazing Accessory Genome in S. pneumoniae

by Bill Hanage
It’s been remarked before, but bacteria are different. Really different. I can think of few more potent demonstrations of this than this new paper that compares accessory genomes in populations of pneumococci – my favorite bug. It is also true that the results of it are so weird that even some of the authors took a while to come to the ‘fall off your chair moment’ as one of them eloquently put it. So I am writing this, in the hope that you will fall off your chair a little earlier than you would have done otherwise. Also if you’re not a bacterial population genomics fan already, I hope this convinces you to become one.

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So you want to learn bioinformatics for bacterial population genomics

by Taj Azarian, Lauren Cowley and Karel Brinda
In the ever-changing world of genomics and epidemiology, technological advancements in sequencing and analysis may often move faster than the workforce can keep up. Here we provide resources for those who want to become more familiar with sequencing, bioinformatics, and population genomic analysis in the emerging field of genomic epidemiology.

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