Extending MetAMOS - new methods and new integrations

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1 Oxford Data Science Centre, Oxford, United Kingdom
2 Department of Bioinformatics, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
3 Applied Research Institute for Prospective Technologies, Vilnius, Lithuania
4 University of Warsaw, Warsaw, Poland
5 Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
6 Faculty of Biology, Uniwersity of Warsaw, Warsaw, Poland
DOI
10.7287/peerj.preprints.1706v1
Published
Accepted
Subject Areas
Bioinformatics, Computational Biology
Keywords
metagenomics, metatranscriptomics, NGS, pipeline, web service
Copyright
© 2016 Siwiak 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
Siwiak M, Bogdanowicz A, Hajduk A, Krassowski M, Jankowski P, Savenko M, Pyzik AA, Szczęsny P. 2016. Extending MetAMOS - new methods and new integrations. PeerJ PrePrints 4:e1706v1

Abstract

Biodiversity analysis of metagenomic and metatranscriptomic data acquired from next-generation sequencing (NGS) requires following multiple analytic steps, often independent from each other with exception of passing output files of previous step as input for the following. If parameterization of steps following one after another is independent from one another, they may be pipelined. There are three most popular pipelines used for NGS analyses: QIIME, mothur and MetAMOS. In this work we describe our extensions to the latter. One is supplementing MetAMOS’ default modes with taxonomic and metabolic biodiversity using metagenomics and metatranscriptomics data and the other provides a web-based interface to run predefined analyses that is easy to integrate with laboratory information management systems.

Author Comment

This is a submission to PeerJ Computer Science for review.