SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.
TLDR
SortMeRNA, a new software designed to rapidly filter rRNA fragments from metatranscriptomic data, is presented, capable of handling large sets of reads and sorting out all fragments matching to the rRNA database with high sensitivity and low running time.Abstract:
MOTIVATION: The application of Next-Generation Sequencing (NGS) technologies to RNAs directly extracted from a community of organisms yields a mixture of fragments characterizing both coding and non-coding types of RNAs. The tasks to distinguish among these and to further categorize the families of messenger RNAs and ribosomal RNAs is an important step for examining gene expression patterns of an interactive environment and the phylogenetic classification of the constituting species. RESULTS: We present SortMeRNA, a new software designed to rapidly filter ribosomal RNA fragments from metatranscriptomic data. It is capable of handling large sets of reads and sorting out all fragments matching to the rRNA database with high sensitivity and low running time. AVAILABILITY: http://bioinfo.lifl.fr/RNA/sortmerna CONTACT: evguenia.kopylova@lifl.fr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.read more
Citations
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Transcriptomic Analysis Reveals Salt Tolerance Mechanisms Present in Date-Plum Persimmon Rootstock (Diospyros lotus L.)
Francisco Gil-Muñoz,Nicolas Delhomme,Ana Quinones,María M. Naval,María Luisa Badenes,M. Rosario García-Gil +5 more
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Arabidopsis thaliana cbp80 , c2h2 , and flk Knockout Mutants Accumulate Increased Amounts of Circular RNAs.
Anna Philips,Katarzyna Nowis,Michal Stelmaszczuk,Jan Podkowiński,Luiza Handschuh,Paulina Jackowiak,Marek Figlerowicz,Marek Figlerowicz +7 more
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Butterfly eyespots evolved via co-option of the antennal gene-regulatory network
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Rapid Expansion of a Highly Germline-Expressed Mariner Element Acquired by Horizontal Transfer in the Fire Ant Genome.
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An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men
Abigail J. S. Armstrong,Michael Shaffer,Nichole M. Nusbacher,Christine Griesmer,Suzanne Fiorillo,Jennifer M. Schneider,C. Preston Neff,Sam X. Li,Andrew P. Fontenot,Thomas B. Campbell,Brent E. Palmer,Catherine A. Lozupone +11 more
TL;DR: This study provides an in-depth characterization of microbiome differences that occur in a US population infected with HIV and demonstrates the degree to which these differences may be driven by lifestyle factors, ART and HIV infection itself.
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