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NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language

View ORCID ProfileLuis Pedro Coelho, View ORCID ProfileRenato Alves, Paulo Monteiro, View ORCID ProfileJaime Huerta-Cepas, View ORCID ProfileAna Teresa Freitas, View ORCID ProfilePeer Bork
doi: https://doi.org/10.1101/367755
Luis Pedro Coelho
1Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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Renato Alves
1Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
2Candidate for Joint PhD degree from EMBL and Heidelberg University, Faculty of Biosciences
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Paulo Monteiro
3INESC-ID, Instituto Superior Técnico, University of Lisbon, Portugal
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Jaime Huerta-Cepas
1Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
4Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
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Ana Teresa Freitas
3INESC-ID, Instituto Superior Técnico, University of Lisbon, Portugal
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  • ORCID record for Ana Teresa Freitas
Peer Bork
1Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
5Max Delbrück Centre for Molecular Medicine, Berlin, Germany
6Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
7Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
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  • For correspondence: bork@embl.de
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Abstract

NGLess is a domain specific language for describing next-generation sequence processing pipelines. It was developed with the goal of enabling user-friendly computational reproducibility.

Using this framework, we developed NG-meta-profiler, a fast profiler for metagenomes which performs sequence preprocessing, mapping to bundled databases, filtering of the mapping results, and profiling (taxonomic and functional). It is significantly faster than either MOCAT2 or htseq-count and (as it builds on NGLess) its results are perfectly reproducible. These pipelines can easily be customized and extended with other tools.

NGLess and NG-meta-profiler are open source software (under the liberal MIT licence) and can be downloaded from http://ngless.embl.de or installed through bioconda.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 13, 2018.
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NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language
Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork
bioRxiv 367755; doi: https://doi.org/10.1101/367755
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NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language
Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork
bioRxiv 367755; doi: https://doi.org/10.1101/367755

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