MetaTrans: an open-source pipeline for metatranscriptomics

Martinez, Xavier; Pozuelo, Marta; Pascal, Victoria; Campos, David; Gut, Ivo Glynne; Gut, Marta; Azpiroz, Fernando; Guarner, Francisco; Manichanh, Chaysavanh

doi:http://dx.doi.org/10.1038/srep26447

MetaTrans: an open-source pipeline for metatranscriptomics

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Citation

Martinez 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/srep26447

Abstract

To 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).