SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.

doi:10.1093/BIOINFORMATICS/BTS611

Open AccessJournal ArticleDOI

SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.

Evguenia Kopylova, +2 more

- 01 Dec 2012 -

Bioinformatics

- Vol. 28, Iss: 24, pp 3211-3217

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.

Citations

PDF

Open Access

More filters

Journal ArticleDOI

A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets

Milkha M. Leimena, +9 more

- 02 Aug 2013 -

BMC Genomics

TL;DR: A reliable pipeline for metatranscriptome data analysis was developed and evaluated using RNA-seq datasets obtained for the human small intestine microbiota, and compared with single- or paired-end sequencing methods indicated that the latter approach does not provide improved functional or phylogenetic insights.

...read moreread less

Journal ArticleDOI

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes.

Romain Blanc-Mathieu, +23 more

- 08 Jun 2017 -

PLOS Genetics

TL;DR: The intriguing parasitic success of asexually-reproducing Meloidogyne species could be partly explained by their TE-rich composite genomes, resulting from allopolyploidization events, and promoting plasticity and functional divergence in the absence of sex and meiosis.

...read moreread less

Journal ArticleDOI

Reproducible protocols for metagenomic analysis of human faecal phageomes.

Andrey N. Shkoporov, +13 more

- 10 Apr 2018 -

Microbiome

TL;DR: A relatively simple, reproducible and cost-efficient protocol for the extraction of viral nucleic acids from human faecal samples, suitable for high-throughput studies and to reduce discrepancies observed within and between research groups studying the human gut phageome.

...read moreread less

Journal ArticleDOI

Planktonic Euryarchaeota are a significant source of archaeal tetraether lipids in the ocean

Sara A. Lincoln, +8 more

- 08 Jul 2014 -

Proceedings of the National Academy of S...

TL;DR: It is found that Marine Group II Euryarchaeota (MG-II) contributed significantly to the tetraether lipid pool in the North Pacific Subtropical Gyre at shallow to intermediate depths, and the data strongly suggested that MG-II also synthesize crenarchaeol, a tetra ether lipid previously considered to be a unique biomarker for ThaumarchAEota.

...read moreread less

Collapse

References

PDF

Open Access

More filters

Journal ArticleDOI

Basic Local Alignment Search Tool

Stephen F. Altschul, +4 more

- 01 Oct 1990 -

Journal of Molecular Biology

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.

...read moreread less

Journal ArticleDOI

Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, +1 more

- 01 Jul 2009 -

Bioinformatics

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.

...read moreread less

Journal ArticleDOI

Search and clustering orders of magnitude faster than BLAST

Robert C. Edgar

- 01 Oct 2010 -

Bioinformatics

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.

...read moreread less

Journal ArticleDOI

ARB: a software environment for sequence data

Wolfgang Ludwig, +31 more

- 15 Mar 2004 -

Nucleic Acids Research

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.

...read moreread less

Journal ArticleDOI

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

Elmar Pruesse, +6 more

- 01 Dec 2007 -

Nucleic Acids Research

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.

...read moreread less