title: MetaTrans: an open-source pipeline for metatranscriptomics.
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).
authors.affiliation: Digestive Research Unit, Vall d'Hebron Research Institute, Barcelona, 08035, Spain.
authors.forename: Xavier
authors.initials: X
authors.lastname: Martinez
authors.affiliation: Digestive Research Unit, Vall d'Hebron Research Institute, Barcelona, 08035, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Pozuelo
authors.affiliation: Digestive Research Unit, Vall d'Hebron Research Institute, Barcelona, 08035, Spain.
authors.forename: Victoria
authors.initials: V
authors.lastname: Pascal
authors.affiliation: Digestive Research Unit, Vall d'Hebron Research Institute, Barcelona, 08035, Spain.
authors.forename: David
authors.initials: D
authors.lastname: Campos
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona, 08028, Spain.|Universitat Pompeu Fabra (UPF), 08002, Barcelona, Spain.
authors.forename: Ivo
authors.initials: I
authors.lastname: Gut
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona, 08028, Spain.|Universitat Pompeu Fabra (UPF), 08002, Barcelona, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Gut
authors.affiliation: Digestive Research Unit, Vall d'Hebron Research Institute, Barcelona, 08035, Spain.|CIBERehd, Instituto de Salud Carlos III, Madrid, 28029, Spain.
authors.forename: Fernando
authors.initials: F
authors.lastname: Azpiroz
authors.affiliation: Digestive Research Unit, Vall d'Hebron Research Institute, Barcelona, 08035, Spain.|CIBERehd, Instituto de Salud Carlos III, Madrid, 28029, Spain.
authors.forename: Francisco
authors.initials: F
authors.lastname: Guarner
authors.affiliation: Digestive Research Unit, Vall d'Hebron Research Institute, Barcelona, 08035, Spain.|CIBERehd, Instituto de Salud Carlos III, Madrid, 28029, Spain.
authors.forename: Chaysavanh
authors.initials: C
authors.lastname: Manichanh
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D005243:Feces / Q000382:microbiology; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020407:Internet; D056186:Metagenomics; D064307:Microbiota; D017423:Sequence Analysis, RNA; D059467:Transcriptome