Martinez, XavierPozuelo, MartaPascal, VictoriaCampos, DavidGut, Ivo GlynneGut, MartaAzpiroz, FernandoGuarner, FranciscoManichanh, Chaysavanh2017-01-272017-01-272016Martinez X, Pozuelo M, Pascal V, Campos D, Gut IG, Gut M, Azpiroz F, Guarner F, Manichanh C. MetaTrans: an open-source pipeline for metatranscriptomics. Scientific Reports. 2016; 6: 26447. DOI: 10.1038/srep264472045-2322http://hdl.handle.net/10230/28008To date, meta-omic approaches use high-throughput sequencing technologies, which produce a huge amount of data, thus challenging modern computers. Here we present MetaTrans, an efficient open-source pipeline to analyze the structure and functions of active microbial communities using the power of multi-threading computers. The pipeline is designed to perform two types of RNA-Seq analyses: taxonomic and gene expression. It performs quality-control assessment, rRNA removal, maps reads against functional databases and also handles differential gene expression analysis. Its efficacy was validated by analyzing data from synthetic mock communities, data from a previous study and data generated from twelve human fecal samples. Compared to an existing web application server, MetaTrans shows more efficiency in terms of runtime (around 2 hours per million of transcripts) and presents adapted tools to compare gene expression levels. It has been tested with a human gut microbiome database but also proposes an option to use a general database in order to analyze other ecosystems. For the installation and use of the pipeline, we provide a detailed guide at the following website (www.metatrans.org).application/pdfeng© Nature Publishing Group. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/articlehttp://dx.doi.org/10.1038/srep26447MicrobiomeTranscriptomicsinfo:eu-repo/semantics/openAccess