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MerCat: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from metagenomic and/or metatranscriptomic sequencing data

, , , , , ,
1 Biological Sciences Division, Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
2 Infomation technology, High Performance Computing (HPC) and Cloud Services, Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
3 Environmental and Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
DOI
10.7287/peerj.preprints.2825v1
Published
Accepted
Subject Areas
Bioinformatics, Computational Biology, Data Science, Scientific Computing and Simulation, Software Engineering
Keywords
K-mer counting, Database-independent property analysis (DIPA), Metagenomic analysis, Metatranscriptomic analysis, Diversity-estimation
Copyright
© 2017 White III et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
White III RA, Panyala A, Glass K, Colby S, Glaesemann KR, Jansson C, Jansson JK. 2017. MerCat: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from metagenomic and/or metatranscriptomic sequencing data. PeerJ Preprints 5:e2825v1

Abstract

MerCat (“ Mer - Cat enate”) is a parallel, highly scalable and modular property software package for robust analysis of features in next-generation sequencing data. Using assembled contigs and raw sequence reads from any platform as input, MerCat performs k-mer counting of any length k, resulting in feature abundance counts tables. MerCat allows for direct analysis of data properties without reference sequence database dependency commonly used by search tools such as BLAST for compositional analysis of whole community shotgun sequencing (e.g., metagenomes and metatranscriptomes).

Author Comment

Initial version of our manuscript submitted for peer review to Bioinformatics

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Richard Allen White III conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, performed the computation work, reviewed drafts of the paper.

Ajay Panyala conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, performed the computation work, reviewed drafts of the paper.

Kevin Glass conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, performed the computation work, reviewed drafts of the paper.

Sean Colby wrote the paper, performed the computation work, reviewed drafts of the paper.

Kurt R Glaesemann conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, wrote the paper, performed the computation work, reviewed drafts of the paper.

Christer Jansson wrote the paper, reviewed drafts of the paper.

Janet K Jansson wrote the paper, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

https://github.com/pnnl/mercat

Funding

This research was provided by PNNL Laboratory-Directed Research and Development (LDRD) Program at PNNL; Microbiomes in Transition (MinT) Initiative, and PNNL Initiative integrated Plant-Atmosphere-Soil System (iPASS; PNNL Project # 204412), a multiprogram national laboratory operated by Battelle for the Department of Energy (DOE) under contract DE-AC06-76RL01830. A portion of the research was conducted using PNNL Institutional Computing (PIC) at PNNL and at EMSL, a national scientific user facility sponsored by the DOE Office of Biological and Environmental Research and located at PNNL. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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MerCat: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from metagenomic and/or metatranscriptomic sequencing data
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