ROCker

Accurately detecting functional genes in metagenomes

ROCker employs Receiver-Operator Curve (ROC)-analysis of in silico generated metagenomic reads that map onto well-curated reference protein sequences, and a sliding window across the length of the reference sequences to deal with non-discriminative domains and motifs that are shared between functionally different proteins.

You can download stand-alone ROCker. If you use ROCker, please cite:

Reference
Orellana LH, Rodriguez-R LM & Konstantinidis KT (under review). Detecting and quantifying functional genes in short-read metagenomic datasets: method development and application to the nitrogen cycle genes.