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The underlying technology or problem is now obsolete and/or superceded by other methods.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

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