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MOCAT2: a metagenomic assembly, annotation and profiling framework.

Jens Roat Kultima1, Luis Pedro Coelho1, Kristoffer Forslund1

  • 1Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.

Bioinformatics (Oxford, England)
|May 7, 2016
PubMed
Summary
This summary is machine-generated.

MOCAT2 is a new software pipeline for metagenomic analysis, improving gene prediction and functional profiling. It enables fast and comprehensive characterization of metagenomes using automated reference catalogs.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Metagenomics

Background:

  • Metagenomic analysis requires efficient tools for sequence assembly and gene prediction.
  • Accurate taxonomic and functional profiling is crucial for understanding microbial communities.

Purpose of the Study:

  • To introduce MOCAT2, a novel software pipeline for metagenomic sequence assembly and gene prediction.
  • To enhance taxonomic and functional abundance profiling in metagenomic data.
  • To facilitate fast and comprehensive functional characterization of metagenomes.

Main Methods:

  • MOCAT2 utilizes automated generation and annotation of non-redundant reference catalogs.
  • Pre-computed assignments from 18 diverse databases are propagated for efficient annotation.
  • The pipeline supports high-performance computing via LSF, PBS, or SGE queuing systems.

Main Results:

  • MOCAT2 provides novel features for taxonomic and functional abundance profiling.
  • Automated catalog generation and annotation enable rapid and thorough metagenome characterization.
  • The software is implemented in Perl 5 and Python 2.7 for 64-bit UNIX systems.

Conclusions:

  • MOCAT2 offers an efficient and comprehensive solution for metagenomic data analysis.
  • The pipeline's features facilitate deeper insights into microbial community functions.
  • MOCAT2 is freely available, promoting accessibility in the research community.