title: COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets.
abstract: BACKGROUND
  Recent advances in sequencing technologies have resulted in an unprecedented increase in the number of metagenomes that are being sequenced world-wide. Given their volume, functional annotation of metagenomic sequence datasets requires specialized computational tools/techniques. In spite of having high accuracy, existing stand-alone functional annotation tools necessitate end-users to perform compute-intensive homology searches of metagenomic datasets against "multiple" databases prior to functional analysis. Although, web-based functional annotation servers address to some extent the problem of availability of compute resources, uploading and analyzing huge volumes of sequence data on a shared public web-service has its own set of limitations. In this study, we present COGNIZER, a comprehensive stand-alone annotation framework which enables end-users to functionally annotate sequences constituting metagenomic datasets. The COGNIZER framework provides multiple workflow options. A subset of these options employs a novel directed-search strategy which helps in reducing the overall compute requirements for end-users. The COGNIZER framework includes a cross-mapping database that enables end-users to simultaneously derive/infer KEGG, Pfam, GO, and SEED subsystem information from the COG annotations.
  
  
  RESULTS
  Validation experiments performed with real-world metagenomes and metatranscriptomes, generated using diverse sequencing technologies, indicate that the novel directed-search strategy employed in COGNIZER helps in reducing the compute requirements without significant loss in annotation accuracy. A comparison of COGNIZER's results with pre-computed benchmark values indicate the reliability of the cross-mapping database employed in COGNIZER.
  
  
  CONCLUSIONS
  The COGNIZER framework is capable of comprehensively annotating any metagenomic or metatranscriptomic dataset from varied sequencing platforms in functional terms. Multiple search options in COGNIZER provide end-users the flexibility of choosing a homology search protocol based on available compute resources. The cross-mapping database in COGNIZER is of high utility since it enables end-users to directly infer/derive KEGG, Pfam, GO, and SEED subsystem annotations from COG categorizations. Furthermore, availability of COGNIZER as a stand-alone scalable implementation is expected to make it a valuable annotation tool in the field of metagenomic research.
  
  
  METHODS
  A Linux implementation of COGNIZER is freely available for download from the following links: http://metagenomics.atc.tcs.com/cognizer, https://metagenomics.atc.tcs.com/function/cognizer.
authors.affiliation: Bio-Sciences R&D Division, TCS Innovation Labs, Tata Consultancy Services Limited, 54-B, Hadapsar Industrial Estate, Pune, 411013, Maharashtra, India.
authors.forename: Tungadri
authors.initials: T
authors.lastname: Bose
authors.affiliation: Bio-Sciences R&D Division, TCS Innovation Labs, Tata Consultancy Services Limited, 54-B, Hadapsar Industrial Estate, Pune, 411013, Maharashtra, India.
authors.forename: Mohammed Monzoorul
authors.initials: MM
authors.lastname: Haque
authors.affiliation: Bio-Sciences R&D Division, TCS Innovation Labs, Tata Consultancy Services Limited, 54-B, Hadapsar Industrial Estate, Pune, 411013, Maharashtra, India.
authors.forename: Cvsk
authors.initials: C
authors.lastname: Reddy
authors.affiliation: Bio-Sciences R&D Division, TCS Innovation Labs, Tata Consultancy Services Limited, 54-B, Hadapsar Industrial Estate, Pune, 411013, Maharashtra, India.
authors.forename: Sharmila S
authors.initials: SS
authors.lastname: Mande
mesh_terms: D000465:Algorithms; D030541:Databases, Genetic; D006801:Humans; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D057188:Workflow