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 storage and analysis of extra-large data, presents an algorithmic solution: the HIVE-hexagon DNA sequence aligner. HIVE-hexagon implements novel approaches to exploit both characteristics of sequence space and CPU, RAM and Input/Output (I/O) architecture to quickly compute accurate alignments. Key components of HIVE-hexagon include non-redundification and sorting of sequences; floating diagonals of linearized dynamic programming matrices; and consideration of cross-similarity to minimize computations. Availability https://hive.biochemistry.gwu.edu/hive/

• Publication year

  2014

• Venue

  PLoS ONE

• Publication date

  2014-06-11

• Fields of study

  Biology, Physics, Computer Science, Environmental Science, Medicine

• Identifiers
  DOI 10.1371/journal.pone.0099033PMID 24918764PMCID 4053384
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• A survey of tools for variant analysis of next-generation genome sequencing data

  2013cited by this paper
• Proteome‐wide analysis of nonsynonymous single‐nucleotide variations in active sites of human proteins

  2013cited by this paper
• Structure-based Comparative Analysis and Prediction of N-linked Glycosylation Sites in Evolutionarily Distant Eukaryotes

  2013cited by this paper
• Data Mining for Bioinformatics

  2012cited by this paper
• Sequence Comparison Alignment-Free Approach Based on Suffix Tree and L-Words Frequency

  2012cited by this paper
• Read length versus Depth of Coverage for Viral Quasispecies Reconstruction

  2012cited by this paper
• Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows

  2012cited by this paper
• GemSIM: general, error-model based simulator of next-generation sequencing data

  2012cited by this paper
• SNVDis: A Proteome-wide Analysis Service for Evaluating nsSNVs in Protein Functional Sites and Pathways

  2012cited by this paper
• Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions

  2011cited by this paper
• Addressing challenges in the production and analysis of illumina sequencing data

  2011cited by this paper
• Storage and Retrieval of Highly Repetitive Sequence Collections

  2010cited by this paper
• A survey of sequence alignment algorithms for next-generation sequencing

  2010cited by this paper
• Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

  2009cited by this paper
• Next-generation sequencing: from basic research to diagnostics.

  2009cited by this paper
• BFAST: An Alignment Tool for Large Scale Genome Resequencing

  2009cited by this paper
• Theory and Mathematical Methods in Bioinformatics

  2008cited by this paper
• Compressed suffix tree - a basis for genome-scale sequence analysis

  2007cited by this paper
• AceView: a comprehensive cDNA-supported gene and transcripts annotation

  2006cited by this paper
• Comparative biosequence metrics

  2005cited by this paper
• WU-Blast2 server at the European Bioinformatics Institute

  2003cited by this paper
• Opportunistic data structures with applications

  2000cited by this paper
• Alignment of whole genomes.

  1999cited by this paper
• Dynamic Programming Alignment Accuracy

  1998cited by this paper
• A Block-sorting Lossless Data Compression Algorithm

  1994cited by this paper
• Generalized suffix trees for biological sequence data: applications and implementation

  1994cited by this paper
• Aligning two sequences within a specified diagonal band

  1992cited by this paper
• A workbench for multiple alignment construction and analysis

  1991cited by this paper
• Basic local alignment search tool.

  1990cited by this paper
• Efficient sequence alignment algorithms.

  1984cited by this paper
• An improved algorithm for matching biological sequences.

  1982cited by this paper
• Identification of common molecular subsequences.

  1981cited by this paper
• Space/time trade-offs in hash coding with allowable errors

  1970cited by this paper
• A general method applicable to the search for similarities in the amino acid sequence of two proteins.

  1970cited by this paper

• Intra-host GI.1 norovirus evolution is shaped by genetic drift and purifying selection.

  2025cites this paper
• GII.17 norovirus re-emerged in the 2020s as a result of dynamic and adaptive evolutionary processes

  2025cites this paper
• Communicating computational workflows in a regulatory environment.

  2024cites this paper
• B cell receptor-induced IL-10 production from neonatal mouse CD19+CD43- cells depends on STAT5-mediated IL-6 secretion

  2023cites this paper
• 5′ copyback defective viral genomes are major component in clinical and non-clinical influenza samples

  2023cites this paper
• Communicating regulatory high-throughput sequencing data using BioCompute Objects.

  2022cites this paper
• Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet

  2022cites this paper
• Tracking ebolavirus genomic drift with a resequencing microarray

  2022cites this paper
• Correction: In search of autophagy biomarkers in breast cancer: Receptor status and drug agnostic transcriptional changes during autophagy flux in cell lines

  2022cites this paper
• Mice with Dysfunctional TGF-β Signaling Develop Altered Intestinal Microbiome and Colorectal Cancer Resistant to 5FU.

  2021cites this paper
• Stable Cell Clones Harboring Self-Replicating SARS-CoV-2 RNAs for Drug Screen

  2021cites this paper
• BioCompute Objects to communicate a viral detection pipeline with potential for use in a regulatory environment

  2021cites this paper
• Bioinformatics tools developed to support BioCompute Objects

  2021influential citation
• Bioinformatics and machine learning in gastrointestinal microbiome research and clinical application.

  2020cites this paper
• Communicating Regulatory High Throughput Sequencing Data Using BioCompute Objects

  2020cites this paper
• Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing

  2020influential citation
• Identification and quantification of defective virus genomes in high throughput sequencing data using DVG-profiler, a novel post-sequence alignment processing algorithm

  2019cites this paper
• Mutated CEACAMs Disrupt Transforming Growth Factor beta Signaling and Alter the Intestinal Microbiome to Promote Colorectal Carcinogenesis.

  2019cites this paper
• SeAlM: A Query Cache Optimization Technique for Next Generation Sequence Alignment

  2019cites this paper
• Baseline human gut microbiota profile in healthy people and standard reporting template

  2018cites this paper
• Sequence comparison of Francisella tularensis LVS, LVS-G and LVS-R.

  2018cites this paper
• A complete Leishmania donovani reference genome identifies novel genetic variations associated with virulence

  2018cites this paper
• Complete Genome Sequence of a Nontypeable GII Norovirus Detected in Peru

  2018cites this paper
• Apache Spark and Hadoop Based Big Data Processing System for Clinical Research

  2018cites this paper
• Comparative Assessment of Alignment Algorithms for NGS Data: Features, Considerations, Implementations, and Future

  2017cites this paper
• Whole genome sequencing of live attenuated Leishmania donovani parasites reveals novel biomarkers of attenuation and enables product characterization

  2017cites this paper
• HIVE-heptagon: A sensible variant-calling algorithm with post-alignment quality controls.

  2017cites this paper
• Separation and assembly of deep sequencing data into discrete sub-population genomes

  2017cites this paper
• Genomic Database Searching.

  2017cites this paper
• A Survey of Bioinformatics-Based Tools in RNA-Sequencing (RNA-Seq) Data Analysis

  2017cites this paper
• Evidence that a polyhexameric genome length is preferred, but not strictly required, for efficient mumps virus replication.

  2016cites this paper
• High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis

  2016cites this paper
• Processing Technology of Massive Human Health Data Based on Hadoop

  2016cites this paper
• Novel computational techniques for mapping and classifying Next-Generation Sequencing data. (Nouvelles techniques informatiques pour la localisation et la classification de données de séquençage haut débit)

  2016cites this paper
• Generation and propagation of recombinant mumps viruses exhibiting an additional U residue in the homopolymeric U tract of the F gene-end signal

  2015cites this paper
• Non-synonymous Single-Nucleotide Variations as Cardiovascular System Disease Biomarkers and Their Roles in Bridging Genomic and Proteomic Technologies

  2015cites this paper
• BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis

  2015cites this paper
• Design and Development of a Medical Big Data Processing System Based on Hadoop

  2015cites this paper
• Census-based rapid and accurate metagenome taxonomic profiling

  2014cites this paper
• CensuScope Algorithm Census-based rapid and accurate metagenome taxonomic profiling

  2014cites this paper
• High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis

  2014cites this paper