Cargando…

RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures

SUMMARY: We propose RabbitKSSD, a high-speed genome distance estimation tool. Specifically, we leverage load-balanced task partitioning, fast I/O, efficient intermediate result accesses, and high-performance data structures to improve overall efficiency. Our performance evaluation demonstrates that...

Descripción completa

Detalles Bibliográficos
Autores principales:	Xu, Xiaoming, Yin, Zekun, Yan, Lifeng, Yi, Huiguang, Wang, Hua, Schmidt, Bertil, Liu, Weiguo
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2023
Materias:	Applications Note
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10681859/ https://www.ncbi.nlm.nih.gov/pubmed/37971961 http://dx.doi.org/10.1093/bioinformatics/btad695

Ejemplares similares

Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis
por: Yi, Huiguang, et al.
Publicado: (2021)

Signed Distance Correlation (SiDCo): an online implementation of distance correlation and partial distance correlation for data-driven network analysis
por: Monti, Francesco, et al.
Publicado: (2023)

RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches
por: Xu, Xiaoming, et al.
Publicado: (2023)

Xwalk: computing and visualizing distances in cross-linking experiments
por: Kahraman, Abdullah, et al.
Publicado: (2011)

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

The systems biology simulation core library
por: Panchiwala, Hemil, et al.
Publicado: (2021)

fqtools: an efficient software suite for modern FASTQ file manipulation
por: Droop, Alastair P.
Publicado: (2016)

Mercator: a pipeline for multi-method, unsupervised visualization and distance generation
por: Abrams, Zachary B., et al.
Publicado: (2021)

DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes
por: van Zundert, G.C.P., et al.
Publicado: (2015)

pyconsFold: a fast and easy tool for modeling and docking using distance predictions
por: Lamb, J, et al.
Publicado: (2021)

GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads
por: Dishuck, Philip C, et al.
Publicado: (2022)

A decoupled, modular and scriptable architecture for tools to curate data platforms
por: Langenstein, Momo, et al.
Publicado: (2021)

GPU accelerated biochemical network simulation
por: Zhou, Yanxiang, et al.
Publicado: (2011)

UniMoG—a unifying framework for genomic distance calculation and sorting based on DCJ
por: Hilker, Rolf, et al.
Publicado: (2012)

pgRNAFinder: a web-based tool to design distance independent paired-gRNA
por: Xiong, Yuanyan, et al.
Publicado: (2017)

Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance
por: Šošić, Martin, et al.
Publicado: (2017)

Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes
por: Muffato, Matthieu, et al.
Publicado: (2010)

FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci
por: Rambaldi, Davide, et al.
Publicado: (2009)

SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal
por: Currat, Mathias, et al.
Publicado: (2019)

Accelerated protein structure comparison using TM-score-GPU
por: Hung, Ling-Hong, et al.
Publicado: (2012)

CD-HIT: accelerated for clustering the next-generation sequencing data
por: Fu, Limin, et al.
Publicado: (2012)

COMER2: GPU-accelerated sensitive and specific homology searches
por: Margelevičius, Mindaugas
Publicado: (2020)

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics
por: Perez-Riverol, Yasset, et al.
Publicado: (2015)

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

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels
por: Jossinet, Fabrice, et al.
Publicado: (2010)

No Promoter Left Behind (NPLB): learn de novo promoter architectures from genome-wide transcription start sites
por: Mitra, Sneha, et al.
Publicado: (2016)

HierCC: a multi-level clustering scheme for population assignments based on core genome MLST
por: Zhou, Zhemin, et al.
Publicado: (2021)

pfsearchV3: a code acceleration and heuristic to search PROSITE profiles
por: Schuepbach, Thierry, et al.
Publicado: (2013)

Development of REDCap-based architecture for a clinical decision support tool linked to the electronic health record for assessment of medication appropriateness
por: Charpentier, Peter A, et al.
Publicado: (2023)

nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing
por: Guizard, Sébastien, et al.
Publicado: (2023)

SMLocalizer, a GPU accelerated ImageJ plugin for single molecule localization microscopy
por: Bernhem, Kristoffer, et al.
Publicado: (2018)

Acceleration of short and long DNA read mapping without loss of accuracy using suffix array
por: Tárraga, Joaquín, et al.
Publicado: (2014)

TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops
por: Milne, Iain, et al.
Publicado: (2009)

itol.toolkit accelerates working with iTOL (Interactive Tree of Life) by an automated generation of annotation files
por: Zhou, Tong, et al.
Publicado: (2023)

rMVP: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool for Genome-wide Association Study
por: Yin, Lilin, et al.
Publicado: (2021)

Building the Frequency Profile of the Core Promoter Element Patterns in the Three ChromHMM Promoter States at 200bp Intervals: A Statistical Perspective
por: Lent, Heather, et al.
Publicado: (2015)

The CroCo cross-link converter: a user-centred tool to convert results from cross-linking mass spectrometry experiments
por: Bender, Julian, et al.
Publicado: (2020)

TEPIC 2—an extended framework for transcription factor binding prediction and integrative epigenomic analysis
por: Schmidt, Florian, et al.
Publicado: (2019)

SMARTS.plus – A Toolbox for Chemical Pattern Design
por: Ehrt, Christiane, et al.
Publicado: (2020)

MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis
por: Matias Rodrigues, João F, et al.
Publicado: (2017)

Cannot write session to /tmp/vufind_sessions/sess_gf5jss5id0b40upfgohu2qfbk7