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The underlying technology or problem is now obsolete and/or superceded by other methods.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