| folder | description |
|---|---|
| /app | web application files |
| /cake | cake framework files |
| /data | example datasets |
| /scripts | Perl and R scripts |
| /doc | documentation |
| /db | relational databases |
| /solr | solr/lucene configuration files |
| /vendors | 3rd-party php tools |
This project is a branch from the original METAREP project (v1.3.4), https://github.com/jcvi/METAREP. Please visit the project's wiki page at http://wiki.github.com/jcvi/METAREP for additional information. The METAREP 1.3.2 installation guide can be found at https://github.com/jcvi/METAREP/wiki/Installation-Guide-v-1.3.2
See changes to METAREP installation in INSTALL.txt
https://github.com/allenlab/PhyloMetarep/blob/master/INSTALL.txt
Additional data, including PhyloDB, can be found here: https://scripps.ucsd.edu/labs/aallen/data
5 min overview
http://www.youtube.com/watch?v=DJNjM7LMVWU
http://www.youtube.com/watch?v=7FPJaPyLjMk&feature=relmfu
http://www.youtube.com/watch?v=j0rlTIkvfvI
De Long vertical ocean depth profile dataset (7 libraries)
http://www.scienceonline.org/cgi/content/full/311/5760/496
JCVI's metagenomics annotation pipeline has been used to annotate the raw reads
http://standardsingenomics.org/index.php/sigen/article/view/sigs.651139