Archive

Alumni

Michael Roach

Research Fellow in Bioinformatics in the Edwards lab and FAME Webmaster

Amber Skye

Honours student in the Dinsdale lab and FAME Webmaster

Back to top ↑

Students

Back to top ↑

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.

Back to top ↑

DeepThought

Back to top ↑

Snakemake

Snaketool and Nektool

Snaketool and Nektool are frameworks for building command line tools using the Snakemake or Nextflow workflow managers

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...

Hecatomb

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

Back to top ↑

Snaketool,

Trimnami

Trim lots of sequencing reads all at once!

Sphae

Phage toolkit to detect and assemble phage candidates for phage therapy.

Snaketool and Nektool

Snaketool and Nektool are frameworks for building command line tools using the Snakemake or Nextflow workflow managers

MetaSnek

MetaSnek is a Python package containing miscellaneous functions for metagenomic pipelines!

Koverage

Koverage lets you quickly and easily get coverage statistics from a collection of reads and an assembly.

Atavide

Atavide is a simple, yet complete workflow for metagenomics data analysis!

Hecatomb

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

Back to top ↑

Snakemake,

Trimnami

Trim lots of sequencing reads all at once!

Sphae

Phage toolkit to detect and assemble phage candidates for phage therapy.

MetaSnek

MetaSnek is a Python package containing miscellaneous functions for metagenomic pipelines!

Koverage

Koverage lets you quickly and easily get coverage statistics from a collection of reads and an assembly.

Atavide

Atavide is a simple, yet complete workflow for metagenomics data analysis!

Back to top ↑

Visiting Scholars

Back to top ↑

Researchers

Nick Falk

Research Associate in Microbiome Research in the Dinsdale lab

Back to top ↑

Phage

Phables

Phables is a tool developed to resolve bacteriophage genomes using phage bubbles in viral metagenomic data.

Phispy

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

PHANOTATE

PHANOTATE is a tool to annotate phage genomes.

Back to top ↑

Hackathon

Back to top ↑

Jupyter

Back to top ↑

Presentation

FAME's fabulous ASM tour

A wrap up of the FAME labs’ trip to the Australian Society for Microbiology conference in Sydney

Back to top ↑

metagenome

MetaSnek

MetaSnek is a Python package containing miscellaneous functions for metagenomic pipelines!

Atavide

Atavide is a simple, yet complete workflow for metagenomics data analysis!

Back to top ↑

phage

Phage genome sequencing for host prediction

Global Phage Host Prediction Consortium White Paper Robert Edwards, Flinders University September 2023 For comment Please contact Rob Edwards (robert.edward...

Phynteny

Phynteny: Synteny-based annotation of bacteriophage genes.

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...

Back to top ↑

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...

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.

Back to top ↑

deepthought

Back to top ↑

annotation

Pharokka

Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.

Back to top ↑

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.

Back to top ↑

Group Leaders

Back to top ↑

Virus

Hecatomb

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

Back to top ↑

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 ...

Back to top ↑

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...

Back to top ↑

Conference

FAME's fabulous ASM tour

A wrap up of the FAME labs’ trip to the Australian Society for Microbiology conference in Sydney

Back to top ↑

git

Back to top ↑

google

Back to top ↑

cloud

Back to top ↑

mmseqs

Searching the NR database with MMSeqs2

We have a computational problem searching the Non-Redundant database, but we can solve that! If you use MMSeqs2 to search the NR database, it needs about 1....

Back to top ↑

mmseqs2

Searching the NR database with MMSeqs2

We have a computational problem searching the Non-Redundant database, but we can solve that! If you use MMSeqs2 to search the NR database, it needs about 1....

Back to top ↑

non-redundant

Searching the NR database with MMSeqs2

We have a computational problem searching the Non-Redundant database, but we can solve that! If you use MMSeqs2 to search the NR database, it needs about 1....

Back to top ↑

database

Searching the NR database with MMSeqs2

We have a computational problem searching the Non-Redundant database, but we can solve that! If you use MMSeqs2 to search the NR database, it needs about 1....

Back to top ↑

QC

Prinseq

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

Back to top ↑

PyCharm

Back to top ↑

Metagenome,

Hecatomb

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

Back to top ↑

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.

Back to top ↑

Prophage

Back to top ↑

IBD

Back to top ↑

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...

Back to top ↑

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...

Back to top ↑

Kraken2

Back to top ↑

superfocus

Back to top ↑

super-focus

Back to top ↑

collaborate

Back to top ↑

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 ...

Back to top ↑

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 ...

Back to top ↑

vpn

Back to top ↑

remote

Back to top ↑

ssh

Back to top ↑

microbiome

Back to top ↑

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 ...

Back to top ↑

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...

Back to top ↑

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...

Back to top ↑

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...

Back to top ↑

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...

Back to top ↑

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...

Back to top ↑

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...

Back to top ↑

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...

Back to top ↑

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...

Back to top ↑

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...

Back to top ↑

genomics

Back to top ↑

SRA

Searching SRA Metadata in the Cloud

This is another in our series of posts on searching things in the SRA. As we noted previously, NCBI has moved most of the SRA into the clouds, which makes se...

Back to top ↑

Google

How to start a Google VM

Starting a Google VM Sometimes you might want to spin up a Google VM to use: WARNING: There maybe charges for starting a VM, running BigQuery searches, or ...

Back to top ↑

sra

Back to top ↑

colabfold

Back to top ↑

workshop

Back to top ↑

teams

Back to top ↑

onedrive

Back to top ↑

microsoft

Back to top ↑

rclone

Back to top ↑

Genome,

Pharokka

Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.

Back to top ↑

bacteria,

Pharokka

Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.

Back to top ↑

metagenomics

Koverage

Koverage lets you quickly and easily get coverage statistics from a collection of reads and an assembly.

Back to top ↑

annotation,

Phynteny

Phynteny: Synteny-based annotation of bacteriophage genes.

Back to top ↑

phage,

Sphae

Phage toolkit to detect and assemble phage candidates for phage therapy.

Back to top ↑

assembly

Sphae

Phage toolkit to detect and assemble phage candidates for phage therapy.

Back to top ↑

read

Trimnami

Trim lots of sequencing reads all at once!

Back to top ↑

trimming,

Trimnami

Trim lots of sequencing reads all at once!

Back to top ↑

qc

Trimnami

Trim lots of sequencing reads all at once!

Back to top ↑

python

Back to top ↑

phyloseq

Back to top ↑

tsv

Back to top ↑

Phage,

Reneo

Reneo means to unravel or untangle in Latin. Reneo is a software developed to unravel or untangle high-quality genomes from viral communities (including both...

Back to top ↑

virus

Reneo

Reneo means to unravel or untangle in Latin. Reneo is a software developed to unravel or untangle high-quality genomes from viral communities (including both...

Back to top ↑

genome

Phage genome sequencing for host prediction

Global Phage Host Prediction Consortium White Paper Robert Edwards, Flinders University September 2023 For comment Please contact Rob Edwards (robert.edward...

Back to top ↑

host

Phage genome sequencing for host prediction

Global Phage Host Prediction Consortium White Paper Robert Edwards, Flinders University September 2023 For comment Please contact Rob Edwards (robert.edward...

Back to top ↑

prediction

Phage genome sequencing for host prediction

Global Phage Host Prediction Consortium White Paper Robert Edwards, Flinders University September 2023 For comment Please contact Rob Edwards (robert.edward...

Back to top ↑

ASM

FAMEous researchers at ASM 2024

Paparazzi spotted FAMEous researchers at Australian Society of Microbiology in Brisbane. Professor Dinsdale chaired the shark infested Environmental Microbes...

Back to top ↑

2024

FAMEous researchers at ASM 2024

Paparazzi spotted FAMEous researchers at Australian Society of Microbiology in Brisbane. Professor Dinsdale chaired the shark infested Environmental Microbes...

Back to top ↑