Home
Here you will find information on individual scripts as well as a tutorial for processing your data. Links to akutils wiki pages are found in the sidebar. Other useful links can be found below.
Using akutils:
Executing any akutils command with no arguments will bring up a usage screen. There are also help screens and this wiki. For a basic walk-through, try the tutorial.
Getting akutils:
See the README file which has detailed documentation: akutils-v1.2 README.
Getting akutils (short instructions):
-
Install Ubuntu14.04LTS. I prefer 14.04.1, and then upgrade manually (step 3).
-
If in a VirtualBox, run this command to allow your screen resolution to expand to your host hardware:
sudo apt-get install virtualbox-guest-x11
-
Run all updates. Don't add anything else just yet.
sudo apt-get update
sudo apt-get -yfm upgrade -
Run the akutils_ubuntu_installation script and follow instructions there.
Useful links:
akutils test data
QIIME
Phyloseq
Vsearch
Swarm
Ghost-tree
NCBI Nucleotide BLAST
HTML reverse/complement tool
Fastx toolkit
ea-utils
Veusz open source plotting software
GraphPad QuickCalcs online stats and such
Citing akutils:
Lela V. Andrews. (2018). akutils-v1.2.4: Facilitating analyses of microbial communities through QIIME. Zenodo. 10.5281/zenodo.1205079
