Rob Edwards

Matthew Flinders Professor in Bioinformatics · Flinders University, Adelaide
Director of Bioinformatics, Flinders Accelerator for Microbiome Exploration (FAME)

I study phages, microbes and metagenomes, and build the software to do it. Most of the tools below run entirely in your web browser: nothing to install, and your data never leaves your computer.

The -viz tools

Open a file and start exploring. These viewers are compiled to WebAssembly or run Python in the browser, so they work on any machine with a modern browser.

GenBankViz

An Artemis-inspired GenBank genome viewer. Browse CDS tracks, inspect qualifiers, zoom and pan across whole genomes, including gzipped and multi-record files.

Open app → Docs Source

bamviz

Drop in a BAM file, pick a contig, and look at the reads mapped to it. Bases are shown as colour when zoomed out and as letters when zoomed in.

Open app → Source

AgViz

View genome assembly graphs in GFA format, with a Bandage-style layout, length-scaled segments, and inspection of segments and links.

Open app → Source

PhiSpyViz

Find prophages in a bacterial genome. Runs the full PhiSpy algorithm in your browser on a GenBank file and shows the predicted prophage regions.

Open app → Source

More browser apps

Converters, design tools, data browsers, and a manuscript editor.

ManuMD New

A Markdown editor for research manuscripts. Live preview, Pandoc citations from your BibTeX library, and load and commit drafts straight to GitHub.

Open app → Source

genbank_to

Convert GenBank files to a swath of other formats, in the browser or on the command line.

Open converter → Source

OligoDesigner

Design random and structured oligos for phage screens, check them for hairpins, homopolymers and repeats, and draw sequence logos.

Open app → Source

PHROG structure gallery

Browse and download predicted structures for representatives of every PHROG phage protein cluster.

Open gallery → Source

Command-line software

Pipelines and tools for phage and metagenome analysis.

Sphae

Phage toolkit for assembling, annotating and screening phage candidates for phage therapy.

GitHub →

PhiSpy

Prediction of prophages in bacterial genomes.

GitHub →

atavide_lite

Metagenome processing with plain Slurm or PBS scripts.

Docs GitHub →

genome_entropy

Compare the entropy of sequences, ORFs, proteins and 3Di encodings.

Docs GitHub →

contigger

Conservative, provenance-aware dereplication and joining of metagenomic contigs.

GitHub →

fastq-pair

Match up paired-end fastq files quickly and efficiently.

GitHub →

PyFBA

Flux balance analysis to model microbial metabolism.

Docs GitHub →

EdwardsLab

A grab bag of lab code: bioinformatics, image analysis and more.

GitHub →

Teaching

Computational Genomics Manual

The manual for my computational genomics and bioinformatics class: hands-on exercises from the command line to genome analysis.

Read the manual → Lecture videos Source