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02 What bioinformatics software not to write part 2
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? [email protected]
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The underlying technology or problem is now obsolete and/or superceded by other methods.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/18XGWpDiaE249qQKDAL7gdBCka0Z1drpA_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/
View all episodes
By Microbial Bioinformatics
5
66 ratings
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? [email protected]
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/18XGWpDiaE249qQKDAL7gdBCka0Z1drpA_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/
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