Software

AAI Calculation

Updated 1 year ago

comparem is a toolbox for comparative genomics. We are using it to calculate AAI (Average Amino Acid Identity) between genomes. It is installed into a conda env within SCGC's anaconda3 module, so to…

ANI Calculation

Updated 1 year ago

The quickest way to calculate ANI is with FastANI. It is available as a module. To load: module use /mod/scgc module load fastani FastANI instructions: $ fastANI --help ----------------- fastANI is a…

Anvi'o

Updated 1 year ago

Anvi'o versions 3, 4 and 5 are installed in their own environments within SCGC's anaconda3 package. To load Anvi'o version 5 type: module load anaconda3 source activate anvio5 To run it interactively…

Conda environments

Updated 1 year ago

If software is available through conda, you can install it yourself into your own anaconda environment. Information on how to create and manage conda environments can be found at this link: https://d…

Jupyter notebook

Updated 6 months ago

To use Jupyter notebooks, you should be on the Bigelow network (either on site or connected to the VPN) Start an interactive session/job qsub -I -q route -l walltime=8:00:00 -l ncpus=2,mem=16G -N jup…

Prokka

Updated 1 year ago

Prokka is available via SCGC's anaconda package. To run: module load anaconda Then prokka is in your path. An example prokka command: prokka --force --outdir {outdirectory} --prefix {prefix} --locust…

RStudio

Updated 1 year ago

Set up X11 forwarding on your local machine To use the RStudio GUI, Charlie allows X11 forwarding. For X forwarding to function, your local machine has to be running an X server program. To set up a…

dada2

Updated 1 year ago

module use /mod/bigelow. module load R/dada2. R. When using the learnErrors function, set multithread equal to the number of cpus available (e.g. 100): learnErrors(filtFs, multithread=100)

sag-mg-recruit

Updated 1 year ago

Metagenomic read recruitment workflow developed by the Stepanauskas Group, used in Pachiadaki et al. 2017. Package github page where extensive instructions can be found: sag-mg-recruit Available on C…

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