Cargando…

METAREP: JCVI metagenomics reports—an open source tool for high-performance comparative metagenomics

Summary: JCVI Metagenomics Reports (METAREP) is a Web 2.0 application designed to help scientists analyze and compare annotated metagenomics datasets. It utilizes Solr/Lucene, a high-performance scalable search engine, to quickly query large data collections. Furthermore, users can use its SQL-like...

Descripción completa

Detalles Bibliográficos
Autores principales:	Goll, Johannes, Rusch, Douglas B., Tanenbaum, David M., Thiagarajan, Mathangi, Li, Kelvin, Methé, Barbara A., Yooseph, Shibu
Formato:	Texto
Lenguaje:	English
Publicado:	Oxford University Press 2010
Materias:	Applications Note
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951084/ https://www.ncbi.nlm.nih.gov/pubmed/20798169 http://dx.doi.org/10.1093/bioinformatics/btq455

Ejemplares similares

A Case Study for Large-Scale Human Microbiome Analysis Using JCVI’s Metagenomics Reports (METAREP)
por: Goll, Johannes, et al.
Publicado: (2012)

The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data
por: Tanenbaum, David M., et al.
Publicado: (2010)

A Metagenomic Framework for the Study of Airborne Microbial Communities
por: Yooseph, Shibu, et al.
Publicado: (2013)

Real Time Metagenomics: Using k-mers to annotate metagenomes
por: Edwards, Robert A., et al.
Publicado: (2012)

Metagenomic Exploration of Viruses throughout the Indian Ocean
por: Williamson, Shannon J., et al.
Publicado: (2012)

MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data
por: Zhu, Zhengwei, et al.
Publicado: (2013)

OrfM: a fast open reading frame predictor for metagenomic data
por: Woodcroft, Ben J., et al.
Publicado: (2016)

NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads
por: Rosen, Gail L., et al.
Publicado: (2011)

Quality control and preprocessing of metagenomic datasets
por: Schmieder, Robert, et al.
Publicado: (2011)

ASAR: visual analysis of metagenomes in R
por: Orakov, Askarbek N, et al.
Publicado: (2018)

Identification of ribosomal RNA genes in metagenomic fragments
por: Huang, Ying, et al.
Publicado: (2009)

Fast and sensitive taxonomic assignment to metagenomic contigs
por: Mirdita, M, et al.
Publicado: (2021)

Simulating Illumina metagenomic data with InSilicoSeq
por: Gourlé, Hadrien, et al.
Publicado: (2019)

WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs
por: Galiez, Clovis, et al.
Publicado: (2017)

SPA: a short peptide assembler for metagenomic data
por: Yang, Youngik, et al.
Publicado: (2013)

MOCAT2: a metagenomic assembly, annotation and profiling framework
por: Kultima, Jens Roat, et al.
Publicado: (2016)

MIDAS2: Metagenomic Intra-species Diversity Analysis System
por: Zhao, Chunyu, et al.
Publicado: (2022)

VirBot: an RNA viral contig detector for metagenomic data
por: Chen, Guowei, et al.
Publicado: (2023)

expam—high-resolution analysis of metagenomes using distance trees
por: Solari, Sean M, et al.
Publicado: (2022)

GOHTAM: a website for ‘Genomic Origin of Horizontal Transfers, Alignment and Metagenomics’
por: Ménigaud, Sabine, et al.
Publicado: (2012)

MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences
por: Tang, Shiyuyun, et al.
Publicado: (2013)

OMARU: a robust and multifaceted pipeline for metagenome-wide association study
por: Kishikawa, Toshihiro, et al.
Publicado: (2022)

metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes
por: Van Rossum, Thea, et al.
Publicado: (2021)

MeganServer: facilitating interactive access to metagenomic data on a server
por: Gautam, Anupam, et al.
Publicado: (2023)

ANDES: Statistical tools for the ANalyses of DEep Sequencing
por: Li, Kelvin, et al.
Publicado: (2010)

Meta-QC-Chain: Comprehensive and Fast Quality Control Method for Metagenomic Data
por: Zhou, Qian, et al.
Publicado: (2014)

MeCorS: Metagenome-enabled error correction of single cell sequencing reads
por: Bremges, Andreas, et al.
Publicado: (2016)

MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs)
por: Stewart, Robert D, et al.
Publicado: (2019)

CAMAMED: a pipeline for composition-aware mapping-based analysis of metagenomic data
por: Norouzi-Beirami, Mohammad H, et al.
Publicado: (2021)

PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences
por: Zielezinski, Andrzej, et al.
Publicado: (2021)

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
por: Abubucker, Sahar, et al.
Publicado: (2012)

Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics
por: Llorens-Marès, Tomàs, et al.
Publicado: (2015)

PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive
por: Torres, Pedro J, et al.
Publicado: (2017)

PlasGUN: gene prediction in plasmid metagenomic short reads using deep learning
por: Fang, Zhencheng, et al.
Publicado: (2020)

SeSaMe: Metagenome Sequence Classification of Arbuscular Mycorrhizal Fungi-associated Microorganisms
por: Eun Kang, Jee, et al.
Publicado: (2020)

nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning
por: Krakau, Sabrina, et al.
Publicado: (2022)

PhaBOX: a web server for identifying and characterizing phage contigs in metagenomic data
por: Shang, Jiayu, et al.
Publicado: (2023)

ProteoWizard: open source software for rapid proteomics tools development
por: Kessner, Darren, et al.
Publicado: (2008)

GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data
por: Calandrelli, Riccardo, et al.
Publicado: (2018)

FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes
por: Niu, Beifang, et al.
Publicado: (2011)

Cannot write session to /tmp/vufind_sessions/sess_moam49cjum7rcopa6f2ltigkes