Cargando…

Querying large read collections in main memory: a versatile data structure

BACKGROUND: High Throughput Sequencing (HTS) is now heavily exploited for genome (re-) sequencing, metagenomics, epigenomics, and transcriptomics and requires different, but computer intensive bioinformatic analyses. When a reference genome is available, mapping reads on it is the first step of this...

Descripción completa

Detalles Bibliográficos
Autores principales:	Philippe, Nicolas, Salson, Mikaël, Lecroq, Thierry, Léonard, Martine, Commes, Thérèse, Rivals, Eric
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2011
Materias:	Methodology Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3163563/ https://www.ncbi.nlm.nih.gov/pubmed/21682852 http://dx.doi.org/10.1186/1471-2105-12-242

Ejemplares similares

CRAC: an integrated approach to the analysis of RNA-seq reads
por: Philippe, Nicolas, et al.
Publicado: (2013)

Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity
por: Philippe, Nicolas, et al.
Publicado: (2009)

Data structures based on k-mers for querying large collections of sequencing data sets
por: Marchet, Camille, et al.
Publicado: (2021)

SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines
por: Audoux, Jérôme, et al.
Publicado: (2017)

Overview of the VA Quality Enhancement Research Initiative (QUERI) and QUERI theme articles: QUERI Series
por: Stetler, Cheryl B, et al.
Publicado: (2008)

DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition
por: Audoux, Jérôme, et al.
Publicado: (2017)

EVA: Exome Variation Analyzer, an efficient and versatile tool for filtering strategies in medical genomics
por: Coutant, Sophie, et al.
Publicado: (2012)

Matching health information seekers' queries to medical terms
por: Soualmia, Lina F, et al.
Publicado: (2012)

Using search queries for malaria surveillance, Thailand
por: Ocampo, Alex J, et al.
Publicado: (2013)

A process for developing an implementation intervention: QUERI Series
por: Curran, Geoffrey M, et al.
Publicado: (2008)

The role of organizational research in implementing evidence-based practice: QUERI Series
por: Yano, Elizabeth M
Publicado: (2008)

Multi-objective database queries in combined knapsack and set covering problem domains
por: Mochocki, Sean A., et al.
Publicado: (2021)

Combined use of cutinase and high-resolution mass-spectrometry to query the molecular architecture of cutin
por: Bhunia, Rupam Kumar, et al.
Publicado: (2018)

Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome
por: Philippe, Nicolas, et al.
Publicado: (2014)

An organizational framework and strategic implementation for system-level change to enhance research-based practice: QUERI Series
por: Stetler, Cheryl B, et al.
Publicado: (2008)

Learning virulent proteins from integrated query networks
por: Cadag, Eithon, et al.
Publicado: (2012)

Scalable long read self-correction and assembly polishing with multiple sequence alignment
por: Morisse, Pierre, et al.
Publicado: (2021)

Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing
por: Giraud, Mathieu, et al.
Publicado: (2014)

ELECTOR: evaluator for long reads correction methods
por: Marchet, Camille, et al.
Publicado: (2019)

Query Lifting: Language-integrated query for heterogeneous nested collections
por: Ricciotti, Wilmer, et al.
Publicado: (2021)

Algorithms for effective querying of compound graph-based pathway databases
por: Dogrusoz, Ugur, et al.
Publicado: (2009)

A versatile web app for identifying the drivers of COVID-19 epidemics
por: Getz, Wayne M., et al.
Publicado: (2021)

Bathometer: lightning fast depth-of-reads query
por: Stenzel, U, et al.
Publicado: (2021)

The Molecule Cloud - compact visualization of large collections of molecules
por: Ertl, Peter, et al.
Publicado: (2012)

Improving high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers
por: Viailly, Pierre-Julien, et al.
Publicado: (2021)

High throughput phenotyping for aphid resistance in large plant collections
por: Chen, Xi, et al.
Publicado: (2012)

UMI-Gen: A UMI-based read simulator for variant calling evaluation in paired-end sequencing NGS libraries
por: Sater, Vincent, et al.
Publicado: (2020)

Sequencing by ligation variation with endonuclease V digestion and deoxyinosine-containing query oligonucleotides
por: Ho, Antoine, et al.
Publicado: (2011)

A new generation of versatile chromogenic substrates for high-throughput analysis of biomass-degrading enzymes
por: Kračun, Stjepan Krešimir, et al.
Publicado: (2015)

A versatile multimodal chromatography strategy to rapidly purify protein nanostructures assembled in cell lysates
por: Winter, Daniel L., et al.
Publicado: (2023)

A fast algorithm for determining the best combination of local alignments to a query sequence
por: Conant, Gavin C, et al.
Publicado: (2004)

The development of an automated sentence generator for the assessment of reading speed
por: Crossland, Michael D, et al.
Publicado: (2008)

Assessing agreement between malaria slide density readings
por: Alexander, Neal, et al.
Publicado: (2010)

Fast and SNP-aware short read alignment with SALT
por: Quan, Wei, et al.
Publicado: (2021)

DPI-ELISA: a fast and versatile method to specify the binding of plant transcription factors to DNA in vitro
por: Brand, Luise H, et al.
Publicado: (2010)

AGROBEST: an efficient Agrobacterium-mediated transient expression method for versatile gene function analyses in Arabidopsis seedlings
por: Wu, Hung-Yi, et al.
Publicado: (2014)

FMLRC: Hybrid long read error correction using an FM-index
por: Wang, Jeremy R., et al.
Publicado: (2018)

Infection of a tomato cell culture by Phytophthora infestans; a versatile tool to study Phytophthora-host interactions
por: Schoina, Charikleia, et al.
Publicado: (2017)

Protocol: a versatile, inexpensive, high-throughput plant genomic DNA extraction method suitable for genotyping-by-sequencing
por: Anderson, Craig B., et al.
Publicado: (2018)

Main characteristics and participation rate of European adolescents included in the HELENA study
por: Béghin, Laurent, et al.
Publicado: (2012)

Cannot write session to /tmp/vufind_sessions/sess_d0d2aleu55m3d5424km3fjjcn3