Cargando…

HIVE-Hexagon: High-Performance, Parallelized Sequence Alignment for Next-Generation Sequencing Data Analysis

Due to the size of Next-Generation Sequencing data, the computational challenge of sequence alignment has been vast. Inexact alignments can take up to 90% of total CPU time in bioinformatics pipelines. High-performance Integrated Virtual Environment (HIVE), a cloud-based environment optimized for st...

Descripción completa

Detalles Bibliográficos
Autores principales:	Santana-Quintero, Luis, Dingerdissen, Hayley, Thierry-Mieg, Jean, Mazumder, Raja, Simonyan, Vahan
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Public Library of Science 2014
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053384/ https://www.ncbi.nlm.nih.gov/pubmed/24918764 http://dx.doi.org/10.1371/journal.pone.0099033

Ejemplares similares

High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis
por: Simonyan, Vahan, et al.
Publicado: (2016)

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis
por: Simonyan, Vahan, et al.
Publicado: (2014)

A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs
por: Dingerdissen, Hayley, et al.
Publicado: (2014)

Human germline and pan-cancer variomes and their distinct functional profiles
por: Pan, Yang, et al.
Publicado: (2014)

Separation and assembly of deep sequencing data into discrete sub-population genomes
por: Karagiannis, Konstantinos, et al.
Publicado: (2017)

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE)
por: Wu, Tsung-Jung, et al.
Publicado: (2014)

HiveRel: hexagons visualization for relationship-based knowledge acquisition
por: Yogev, Sivan, et al.
Publicado: (2022)

Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing
por: Mane, Shrinivasrao P, et al.
Publicado: (2009)

Identification and quantification of defective virus genomes in high throughput sequencing data using DVG-profiler, a novel post-sequence alignment processing algorithm
por: Bosma, Trent J., et al.
Publicado: (2019)

SNVDis: A Proteome-wide Analysis Service for Evaluating nsSNVs in Protein Functional Sites and Pathways
por: Karagiannis, Konstantinos, et al.
Publicado: (2013)

Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing
por: Hora, Bhavna, et al.
Publicado: (2020)

Next generation sequencing reads comparison with an alignment-free distance
por: Weitschek, Emanuel, et al.
Publicado: (2014)

Bit-parallel sequence-to-graph alignment
por: Rautiainen, Mikko, et al.
Publicado: (2019)

AB079. A next generation sequencing parallel biopsy protocol
por: Li, Jing, et al.
Publicado: (2018)

BamView: visualizing and interpretation of next-generation sequencing read alignments
por: Carver, Tim, et al.
Publicado: (2013)

Evaluation and Comparison of Multiple Aligners for Next-Generation Sequencing Data Analysis
por: Shang, Jing, et al.
Publicado: (2014)

Parallelization of the MAFFT multiple sequence alignment program
por: Katoh, Kazutaka, et al.
Publicado: (2010)

Considerations for clinical read alignment and mutational profiling using next-generation sequencing
por: Oliver, Gavin R
Publicado: (2012)

Parallel progressive multiple sequence alignment on reconfigurable meshes
por: Nguyen, Ken D, et al.
Publicado: (2011)

Parallelization of MAFFT for large-scale multiple sequence alignments
por: Nakamura, Tsukasa, et al.
Publicado: (2018)

Programming Hive
por: Capriolo, Edward, et al.
Publicado: (2012)

Hive (hands on)
por: BARANOWSKI, Zbigniew
Publicado: (2015)

The Bees and the Hive
Publicado: (1888)

Next-Generation Sequencing
por: Xiong, Momiao, et al.
Publicado: (2010)

Next-generation sequencing
por: Reis-Filho, Jorge S
Publicado: (2009)

Aligning to the sample-specific reference sequence to optimize the accuracy of next-generation sequencing analysis for hepatitis B virus
por: Liu, Wen-Chun, et al.
Publicado: (2015)

GeoDanceHive: An Operational Hive for Honeybees Dances Recording
por: Galopin, Sylvain, et al.
Publicado: (2023)

Identification of radiation-induced microRNA transcriptome by next-generation massively parallel sequencing
por: Chaudhry, M. Ahmad, et al.
Publicado: (2013)

girafe – an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads
por: Toedling, Joern, et al.
Publicado: (2010)

Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data
por: Kosugi, Shunichi, et al.
Publicado: (2013)

Multi-genome alignment for quality control and contamination screening of next-generation sequencing data
por: Hadfield, James, et al.
Publicado: (2014)

An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data
por: Fan, Huan, et al.
Publicado: (2015)

A fast read alignment method based on seed-and-vote for next generation sequencing
por: Liu, Song, et al.
Publicado: (2016)

BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery
por: Dingerdissen, Hayley M, et al.
Publicado: (2018)

Loss and gain of N-linked glycosylation sequons due to single-nucleotide variation in cancer
por: Fan, Yu, et al.
Publicado: (2018)

Next-Generation Sequencing and Genome Editing in Plant Virology
por: Hadidi, Ahmed, et al.
Publicado: (2016)

Genome Sequence of Mycoplasma hyorhinis Strain DBS 1050
por: Dabrazhynetskaya, Alena, et al.
Publicado: (2014)

Parallelized pairwise sequence alignment using CUDA on multiple GPUs
por: Jung, Sungbo
Publicado: (2009)

Magic-BLAST, an accurate RNA-seq aligner for long and short reads
por: Boratyn, Grzegorz M., et al.
Publicado: (2019)

LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences
por: Winkler, Jörg, et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_5mu5agbljtd4mgd7n8feijhkcl