Archive

Students

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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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DeepThought

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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.

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Researchers

Nick Falk

Research Associate in Microbiome Research in the Dinsdale lab

Michael Roach

Research Fellow in Bioinformatics in the Edwards lab and FAME webmaster

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Snaketool,

Trimnami

Trim lots of sequencing reads all at once!

Spae

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.

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Alumni

Amber Skye

Honours student in the Dinsdale lab and FAME Webmaster

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Snakemake,

Trimnami

Trim lots of sequencing reads all at once!

Spae

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!

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Visiting Scholars

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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.

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Hackathon

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Jupyter

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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!

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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...

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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Presentation

FAME's fabulous ASM tour

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

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deepthought

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annotation

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phage

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...

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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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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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Virus

Hecatomb

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

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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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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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git

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google

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cloud

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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....

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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....

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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....

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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....

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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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Metagenome,

Hecatomb

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

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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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Prophage

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IBD

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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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microbiome

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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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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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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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genomics

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Conference

FAME's fabulous ASM tour

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

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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...

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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 ...

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sra

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colabfold

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workshop

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teams

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onedrive

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microsoft

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rclone

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Genome,

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bacteria,

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metagenomics

Koverage

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

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annotation,

Phynteny

Phynteny: Synteny-based annotation of bacteriophage genes.

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phage,

Spae

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

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assembly

Spae

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

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read

Trimnami

Trim lots of sequencing reads all at once!

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trimming,

Trimnami

Trim lots of sequencing reads all at once!

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qc

Trimnami

Trim lots of sequencing reads all at once!

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python

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phyloseq

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tsv

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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...

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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...

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