Notes on Origin as CAMERA Metagenomic Annotation Pipeline
=========================================================

I've forked this repo from one deposited by Joshua Orvis to Github.

Much of the code here was developed by Brett Whitty at JCVI in 2007 as part of the CAMERA metagenomic annotation pipeline, and presumably was exported from JCVI's internal SVN repository where I left it as of January 2008.

The development of the CAMERA metagenomic annotation pipeline and related infrastructure leading up to the CAMERA 1.0 release in December/January of 2007/8 was described in an internal presentation I gave before departing JCVI in Jan 2008 that I've made available on Slideshare:

https://www.slideshare.net/BrettWhitty/camera-metagenomic-annotation-pipeline

Highlights include my idea to decouple the filtering of analysis results to prepare filtered/canonized annotation data types (ie: parsing step) from the application of an annotation rules set/hierarchy to prepare "final" annotation (ie: rules step); quick and dirty implementation of the annotation rules using extendable operators and handler functions; general object-oriented approach, which made sense to me at the time and I think proved to make the code pretty flexible for subsequent use; fun use of GNU sort for merging results from different analysis types before applying rules --- was hugely faster to dump to dump annotation objects to flat files and merge in this way.

You'll find the subsequent published revision of these software and methods described in the 2010 SIGS paper "The JCVI standard operating procedure for annotating metagenomic shotgun sequencing data" under 'docs'.

- Brett Whitty, 2017

(Contents of original README follows)
--

JCVI Metagenomics Annotation Pipline
-------------------------------------------------------
File Structure

bin       perl binaries
data      lookup files
example   example files (contains test set)
lib       perl library files