micro

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The underlying technology or problem is now obsolete and/or superceded by other methods. 

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/

01 What bioinformatics software not to write part 1

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 from the University of Oxford (UK), and Prof. Andrew Page from Theiagen Genomics (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, University of Oxford or Theiagen Genomics.

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/

Question and comments? microbinfie@gmail.com

01 What bioinformatics software not to write part 1

Micro Binfie Podcast