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 (2016). ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores. Nucleic Acids Research 45 (3): e14.