Archive

Students

Amber Skye

Honours student in the Dinsdale lab and FAME Webmaster

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Tutorial

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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Researchers

Sarah Giles

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

Michael Roach

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

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DeepThought

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Snakemake

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...

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Phage

Phispy

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

PHANOTATE

PHANOTATE is a tool to annotate phage genomes.

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Metagenome

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...

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

FOCUS

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

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Conda

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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Regular meetings

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Group Leaders

Rob Edwards

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

Liz Dinsdale

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

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IBD

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Prophage

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Jupyter

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Virus

Hecatomb

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

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deepthought

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QC

Prinseq

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

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PyCharm

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Upcoming events

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Linux

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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Presentation

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Checkpoints

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...

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Deepthought

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...

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Kraken2

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superfocus

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super-focus

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collaborate

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qiime2

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 ...

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conda

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 ...

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vpn

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remote

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ssh

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metagenome

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microbiome

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annotation

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atavide

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 ...

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R

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 ...

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Past presentations

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turbocor

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...

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pearson

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...

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correlation

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...

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statistics

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...

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ncbi

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...

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ncbi_dataset

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...

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alphafold

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...

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phage

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...

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lambda

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...

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Krona

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...

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FOCUS

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...

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