Ants, Bees, Genomes & Evolution @ Queen Mary University London

Major bioinformatic software tools that we develop include:

SequenceServer - implement, visualize & interpret BLAST analyses

SequenceServer - implement, visualize & interpret BLAST analyses

SequenceServer - implement, visualize & interpret BLAST analyses
CompareGenomeQualities - figure out which genome assembly is the best

CompareGenomeQualities - figure out which genome assembly is the best

  • CompareGenomeQualities ranks assemblies based on contiguity, completeness, and accuracy. Contiguity is assessed through NG50 metric. Completeness and accuracy are assessed in genic regions using BUSCO and genome-wide using short Illumina reads. The tool is flexible, easy to run, and provides useful output visualisation.
  • Parameter exploration improves the accuracy of long-read genome assembly.
CompareGenomeQualities - figure out which genome assembly is the best
Flo - transfer existing gene predictions to a new genome assembly

Flo - transfer existing gene predictions to a new genome assembly

  • Flo enables you to 'lift over' the gene prediction and other annotations from a GFF file to a new genome assembly. This is similar to UCSC LiftOver and NCBI LiftUp, but works with unpublished data on any species. It is multithreaded to ensure that it runs fast.
Flo - transfer existing gene predictions to a new genome assembly
GeneValidator - choose the best gene models

GeneValidator - choose the best gene models

GeneValidator - choose the best gene models
TGNet - evalutate genome quality with an independent transcriptome

TGNet - evalutate genome quality with an independent transcriptome

TGNet - evalutate genome quality with an independent transcriptome
Fourmidable / antgenomes.org

Fourmidable / antgenomes.org

Fourmidable / antgenomes.org


Software development approaches

We believe in Reproducible Research & Software Sustainability. When possible we respect style guides and use unit testing & continuous integration. We aim to respect these approaches in our research on specific biological questions and in our tool development. We develop mostly in:

But we love quick and dirty hacks too .

A lot of our code is at https://github.com/wurmlab.



Some tools now have limited relevance

oSwitch has been superceded by updates in docker. Afra has been used in our MSc course; it is currently somewhat out of sync with main Apollo.

BioNode
BioNode
oswitch

oswitch

oswitch
Afra

Afra

Afra