Software
Here is a list of the research software I have developed around metagenomic binning, viral genome reconstruction, scientific workflows, scientific data visualisation and web-based analytics since my PhD.
Research Software
GraphBin
The first automated tool to use assembly graphs to refine binning results from metagenomic contig-binning tools.
- Stars
- 98
- Forks
- 10
- Downloads
- 8.0k
GraphBin2
A next-generation GraphBin approach that refines bins and assigns contigs to multiple bins when shared between species.
- Stars
- 37
- Forks
- 4
- Downloads
- 3.1k
GraphBin-Tk
An assembly graph-based metagenomic binning toolkit that combines GraphBin, GraphBin2, MetaCoAG, visualisation, and evaluation.
- Stars
- 24
- Forks
- 6
- Downloads
- 1.6k
MetaCoAG
A stand-alone metagenomic contig-binning tool that uses assembly graphs alongside composition and coverage.
- Stars
- 69
- Forks
- 7
- Downloads
- 12.4k
agtools
A Python framework for manipulating assembly graphs for downstream metagenomic applications, with a focus on the GFA format.
- Stars
- 21
- Forks
- 3
- Downloads
- 1.6k
ConDiGA
A contigs directed gene annotation pipeline for protein sequence database construction in metaproteomics.
- Stars
- 7
- Forks
- 2
- Downloads
- 2.0k
Phables
A tool for resolving high-quality bacteriophage genomes from fragmented viral metagenomic assemblies.
- Stars
- 86
- Forks
- 7
- Downloads
- 23.5k
Reneo
Software for untangling high-quality genomes from viral communities found within metagenomes.
- Stars
- 11
- Forks
- 2
- Downloads
- 5.6k
Web Applications
GraphBin-Viz
A browser-based interactive visual analytics framework for exploring and comparing metagenomic binning results on assembly graphs.
- Stars
- 7
- Forks
- 2
PhageScale
A browser-based app for measuring bacteriophage capsid diameter and tail length from transmission electron microscopy images.
- Stars
- 0
- Forks
- 0