MOCAT2: a metagenomic assembly, annotation and profiling framework

Bioinformatics. 2016 Aug 15;32(16):2520-3. doi: 10.1093/bioinformatics/btw183. Epub 2016 Apr 8.


MOCAT2 is a software pipeline for metagenomic sequence assembly and gene prediction with novel features for taxonomic and functional abundance profiling. The automated generation and efficient annotation of non-redundant reference catalogs by propagating pre-computed assignments from 18 databases covering various functional categories allows for fast and comprehensive functional characterization of metagenomes.

Availability and implementation: MOCAT2 is implemented in Perl 5 and Python 2.7, designed for 64-bit UNIX systems and offers support for high-performance computer usage via LSF, PBS or SGE queuing systems; source code is freely available under the GPL3 license at

Contact: :

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Databases, Factual
  • Metagenome
  • Metagenomics*
  • Software*