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Krona plots are easy (metagenomics example)

Krona plots are a fantastic way of representing heirarchial data such as taxonomic annotations. These plots are interactive, visually appealing, and best of...

Running AlphaFold on phage lambda

DeepMind’s AlphaFold is winning at predicting tertiary structures from primary amino acid sequences. We thought it would be fun to investigate how it perfo...

NCBI datasets and genome assembly data

Recently, NCBI released their new datasets API that might replace NCBI E-utils. At the moment, datasets is focused on genomes, genes, and viruses, but no dou...

Fast correlations with turbocor

We often want to calculate Pearson correlation between different datasets, for example, we have used it to identify the hosts of different phages. Often, we...

Atavide: importing your data into R

This post is one of a multipart series about analysing your metagenomics samples with Atavide. It is intended to be a quick and dirty look at the superfocus ...

How to install qiime2 on deepthought

Why would I want to do this? I am not really sure, but if you want to use Qiime2 you should install it on deepthought using conda. The sysadmins (may they ...

Snakemake profiles updated

This is an update from a previous post https://fame.flinders.edu.au/blog/2020/09/04/snakemakeprofile where Rob outlines a simple Snakemake profile for runnin...

How to use Snakemake Checkpoints

Snakemake checkpoints are a little complex to get your head around, and so here are two examples that will hopefully clarify some use cases. Before we begin...

Getting started with linux

It can be daunting when you’re just starting out using the Linux command line to access the University’s HPC resources.

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People

Sarah Giles

Postdoctoral Research Associate as part of the FAME laboratory at Flinders University

Rob Edwards

Rob is the Director of Bioinformatics and Human Microbiology for FAME.

Michael Roach

Research Associate in Bioinformatics in Rob Edwards’ lab and FAME webmaster

Liz Dinsdale

My research uses genomics to investigate the biodiversity and ecology of microbes and viruses on coral reefs, kelp forest and shark epidermis.

Amber Skye

Honours student in the Dinsdale lab and FAME Webmaster

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Software

Hecatomb

Hecatomb is a pipeline for accurately classifying viral sequences in metagenome samples.

SUPER-FOCUS

SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data

Prinseq

PRINSEQ is used for easy and rapid quality control and data preprocessing of genomic and metagenomic datasets.

Phispy

PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes.

PHANOTATE

PHANOTATE is a tool to annotate phage genomes.

FOCUS

FOCUS: An Alignment-Free Model To Identify Organisms In Metagenomes Using Non-Negative Least Squares Usage.

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Events

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Projects

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