Micro binfie podcast

So it's the end of 2019 and we thought we'd like to pause and look back at what we were working on . What resonated with us and where we think the micro binfie field will go in the new year.

This episode we discuss the ubiquitous Sequence Alignment Map (SAM)format

Torsten Seemann joins us to discuss how to write good bioinformatics software. Torsten is the author of many popular bioinformatics tools such as Prokka, Snippy, Barrnap, Abricate, Shovill, and Nullarbor.

Links:

https://github.com/tseemann

Modern genotyping is discussed in this second part.

Genotyping is at the foundation of modern microbiology. We discuss all of the techniques used in the preNGS era.

FASTQ files are the foundation of modern bioinformatics. Tune into an informal chat between Lee, Nabil and Andrew as they tell the story of how FASTQs evolved out of nowhere, with all the backstories and qwerks. You might even learn something.

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The underlying technology or problem is now obsolete and/or superceded by other methods.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/

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 genome assembly, read mapping and phylogenetics.

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.

Multiple sequence aligners:

MAFFT https://mafft.cbrc.jp/alignment/software/

MUSCLE https://www.drive5.com/muscle/

Whole genome aligners:

Mauve http://darlinglab.org/mauve/mauve.html

Mugsy http://mugsy.sourceforge.net/

Sibellia http://bioinf.spbau.ru/sibelia

Parsnp https://github.com/marbl/parsnp

Assemblers:

SPADES https://github.com/ablab/spades

Skesa https://github.com/ncbi/SKESA

Velvet https://www.ebi.ac.uk/~zerbino/velvet/

Abyss https://github.com/bcgsc/abyss

Edena http://www.genomic.ch/edena.php

Ray http://denovoassembler.sourceforge.net/

Long read assemblies

HGAP https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/HGAP-2.0

Flye https://github.com/fenderglass/Flye

Canu https://github.com/marbl/canu

Ra https://www.biorxiv.org/content/10.1101/656306v1

Unicycler https://github.com/rrwick/Unicycler

Read mapping

BWA http://bio-bwa.sourceforge.net/

Bowtie2 http://bio-bwa.sourceforge.net/

Minimap2 https://github.com/lh3/minimap2 (BWA better for short reads: https://lh3.github.io/2018/04/02/minimap2-and-the-future-of-bwa)

BBtools https://jgi.doe.gov/data-and-tools/bbtools/

BLAST/BLAT: https://genome.ucsc.edu/FAQ/FAQblat.html

SMALT https://www.sanger.ac.uk/science/tools/smalt-0

Snippy https://github.com/tseemann/snippy

Phenix: https://github.com/phe-bioinformatics/PHEnix

Variant callers

GATK: https://software.broadinstitute.org/gatk/

VIPR: https://www.viprbrc.org/brc/home.spg?decorator=vipr

Varscan2 http://varscan.sourceforge.net/

Workflow managers

Bespoke example https://github.com/VertebrateResequencing/vr-codebase

Snakemake. https://snakemake.readthedocs.io/en/stable/

Nextflow https://www.nextflow.io/

Galaxy https://usegalaxy.org/

Bpipe https://github.com/ssadedin/bpipe

Phylogenetics:

Raxml - Raxml-NG https://cme.h-its.org/exelixis/software.html

IQTREE http://www.iqtree.org/

FastTree http://www.microbesonline.org/fasttree/

BEAST 1&2 https://www.beast2.org/

RevBayes https://revbayes.github.io/

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

Other mentioned resources

Mentioned Recent review.

Zhang W, Chen J, Yang Y, Tang Y, Shang J, Shen B (2011) A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies. PLoS ONE 6(3): e17915. https://doi.org/10.1371/journal.pone.0017915

The Assemblerthon: https://assemblathon.org/

Blog post describing that BWA better for short reads: https://lh3.github.io/2018/04/02/minimap2-and-the-future-of-bwa

The science web: https://thescienceweb.wordpress.com/2015/03/23/each-bioinformatician-to-have-their-own-personal-short-read-aligner-by-2016/

The Micro Binfie poscast is available at SoundCloud (https://soundcloud.com/microbinfie)

or you can subscribe via iTunes: https://podcasts.apple.com/au/podcast/microbinfie-podcast/id1479852809

or Spotify: https://podcasters.spotify.com/podcast/2zuzT8EVxbU0yOGFDVareK

or your favourite podcast software.