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Welcome to the akutils wiki!
This repository is no longer maintained.
These are scripts I wrote to become more productive in processing MiSeq amplicon data for my dissertation. I am screening 16S (515F/806R) and ITS2 (primers not yet published) and sometimes work on other loci for other people (eg LSU, SSU, nifH).
Calling any script with no argument will display usage (except a few) and all scripts have --help and -h functionality.
My system that everything has been tested on:
Hardware: 2012 MacPro, dual 6-core Intel Xeon E5645 @ 2.4GHz with hyperthreading (24 usable cores), 64GB RAM, 3TB internal RAID1, 22TB external hybrid RAID. OS: Ubuntu Linux 14.04LTS 64bit. Software: QIIME 1.9.0 and many useful accessories...
I also try to test scripts on the monsoon compute cluster at NAU which runs Centos 6.6.
If your system is terribly different from mine (OS mainly), these scripts might not work very well for you. If they do work, it is probably worthwhile to do a fresh git pull command about once a week as I am regularly tweaking these scripts to be more efficient, provide more meaningful output, and to stay functional as various dependencies change.
For installation instructions, see the README at the akutils home (scroll down below the file list).
Use the sidebar to navigate through the script pages or use the akutils_command_list.sh page.