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
More filters
Journal ArticleDOI
Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition
Caroline Belser,Julie Poulain,Karine Labadie,Frédérick Gavory,Adriana Alberti,Julie Guy,Quentin Carradec,Corinne Cruaud,Corinne Da Silva,Stefan Engelen,Paul Mielle,Aude C Perdereau,Gaelle Samson,S. Gas,Christian R. Voolstra,Pierre E. Galand,Juana M. Flores,Benjamin C. C. Hume,Gabriela Perna,Maren Ziegler,Hans-Joachim Ruscheweyh,Emilie Boissin,Sarah Romac,Guillaume Bourdin,Guillaume Iwankow,Clémentine Moulin,Sylvain Agostini,Bernard Banaigs,Emmanuel Boss,Chris Bowler,Colomban de Vargas,Eric Douville,Didier Forcioli,Paola Furla,Eric Gilson,Fabien Lombard,Stephane Pesant,Stéphanie Reynaud,Shinichi Sunagawa,Olivier P. Thomas,Romain Troublé,Rebecca Vega Thurber,Didier Zoccola,Claude Scarpelli,E'Krame Jacoby,Pedro Henrique Francisco de Oliveira,Jean-Marc Aury,Denis Allemand,Serge Planes,Patrick Wincker +49 more
TL;DR: Tara Pacific as discussed by the authors is a multi-omics workflow for coral reef data generation, from sample handling to nucleotide sequence data generation and deposition, which includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reefs dynamics and their fate in the Anthropocene.
Journal ArticleDOI
Complete Genome Sequence of Bovine Polyomavirus Type 1 from Aborted Cattle, Isolated in Belgium in 2014
Steven Van Borm,Toon Rosseel,Isabelle Behaeghel,Marc Saulmont,Laurent Delooz,Thierry Petitjean,Elisabeth Mathijs,Frank P.H.A. Vandenbussche +7 more
TL;DR: The complete and fully annotated genome sequence of a bovine polyomavirus type 1 (BPyV/BEL/1/2014) from aborted cattle was assembled from a metagenomics data set.
Journal ArticleDOI
Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments
TL;DR: While data-processing tools require further exploration, total RNA-Seq might be a favorable alternative to metagenomics for target-PCR-free taxonomic identifications of microbial communities and might enable a substantial reduction in sequencing costs while maintaining accuracy.
Posted ContentDOI
Arthropods and the evolution of RNA viruses
TL;DR: The authors mined meta-transcriptomes from 711 arthropod species, including insects, arachnids, myriapods, and crustaceans, and uncovered more than 1400 previously unknown RNA viruses, representing 822 novel evolutionary groups at a level between species and genus.
Journal ArticleDOI
Deep-amplicon sequencing (DAS) analysis to determine the presence of pathogenic Helicobacter species in wastewater reused for irrigation.
TL;DR: The different molecular techniques used in the present study provided evidence, for the first time, of the presence of species belonging to the genus Helicobacter such as H. pylori,H.
References
More filters
Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Journal ArticleDOI
Search and clustering orders of magnitude faster than BLAST
TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Journal ArticleDOI
ARB: a software environment for sequence data
Wolfgang Ludwig,Oliver Strunk,Ralf Westram,Lothar Richter,Harald Meier,Yadhukumar,Arno Buchner,Tina Lai,Susanne Steppi,Gangolf Jobb,Wolfram Förster,Igor Brettske,Stefan Gerber,Anton W. Ginhart,Oliver Gross,Silke Grumann,Stefan Hermann,Ralf Jost,Andreas König,Thomas Liss,Ralph Lüßmann,Michael May,Björn Nonhoff,Boris Reichel,Robert Strehlow,Alexandros Stamatakis,Norbert Stuckmann,Alexander Vilbig,Michael Lenke,Thomas Ludwig,Arndt Bode,Karl-Heinz Schleifer +31 more
TL;DR: The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface.
Journal ArticleDOI
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
Elmar Pruesse,Christian Quast,Katrin Knittel,Bernhard M. Fuchs,Wolfgang Ludwig,Jörg Peplies,Frank Oliver Glöckner +6 more
TL;DR: SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains.
Related Papers (5)
Trimmomatic: a flexible trimmer for Illumina sequence data
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more