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Nabil-Fareed Alikhan

MicroBinfie Podcast, 02 What bioinformatics software not to write part 2

microbinfie, podcast1 min read

In this episode we identify areas of “Peak-bioinformatics”. There are a lot of existing bioinformatics software out there - more often than not the new tool you want to write already exists or a new tool cannot effectively improve. We discuss this in terms of metagenomics and anti microbial resistance. Question and comments? microbinfie@gmail.com SHOW NOTES Generally, novel software is not needed if: There are a plethora of existing tools The problem is more or less solved or its been shown to be unsolvable The underlying technology or problem is now obsolete and/or superceded by other methods. Metagenomics Taxonomic classification: Megan, Kraken, SIGMA, MIDAS, metaphlan2, mOTUs. Assemblers: MetaSpades, metaflye,MEGAHIT, MetaVelvet, a lot of single isolate assemblers have been tweaked to run on metagenomes. https://github.com/lskatz/Kalamari AMR https://github.com/arpcard/amr_curation https://food-safety- bioinformatics-hackathon.github.io/AMR-protocols/ ABRICATE https://github.com/tseemann/abricate ARIBA https://www.sanger.ac.uk/science/tools/ariba Too many detection tools: https://docs.google.com/spreadsheets/d/18XGWpDiaE249qQKDAL7gdBC ka0Z1drpA_s3FElfMJe0/edit#gid=0 Microbial Bioinformatics is a rapidly changing field marrying computer science and microbiology. Join us as we share some tips and tricks we've learnt over the years. If you're student just getting to grips to the field, or someone who just wants to keep tabs on the latest and greatest - this podcast is for you. The hosts are Dr. Lee Katz from the Centres for Disease Control and Prevention (US), Dr. Nabil-Fareed Alikhan and Dr. Andrew Page both from Quadram Institute Bioscience (UK) and bring together years of experience in microbial bioinformatics. The opinions expressed here are our own and do not necessarily reflect the views of Centres for Disease Control and Prevention or Quadram Institute Bioscience. Intro music : Werq - Kevin MacLeod (incompetech.com) Licensed under Creative Commons: By Attribution 3.0 License http://creativecommons.org/licenses/by/3.0/ Outro music : Scheming Weasel (faster version) - Kevin MacLeod (incompetech.com) Licensed under Creative Commons: By Attribution 3.0 License http://creativecommons.org/licenses/by/3.0/