2026-04-17T06:13:28Zhttps://recercat.cat/oai/request

oai:recercat.cat:10230/280082025-12-12T03:13:36Zcom_2072_6col_2072_452952

00925njm 22002777a 4500 dc Martinez, Xavier author Pozuelo, Marta author Pascal, Victoria author Campos, David author Gut, Ivo Glynne author Gut, Marta author Azpiroz, Fernando author Guarner, Francisco author Manichanh, Chaysavanh author 2017-01-27T08:53:42Z 2017-01-27T08:53:42Z 2016 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). Microbiome Transcriptomics MetaTrans: an open-source pipeline for metatranscriptomics