Accelerating 3D genomics data analysis with Microcket.

Genomics / methods Software High-Throughput Nucleotide Sequencing / methods Humans Sequence Analysis, DNA / methods Data Analysis

Journal

Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179

Informations de publication

Date de publication:
01 Jun 2024
Historique:
received: 27 03 2024
accepted: 24 05 2024
medline: 2 6 2024
pubmed: 2 6 2024
entrez: 1 6 2024
Statut: epublish

Résumé

The three-dimensional (3D) organization of genome is fundamental to cell biology. To explore 3D genome, emerging high-throughput approaches have produced billions of sequencing reads, which is challenging and time-consuming to analyze. Here we present Microcket, a package for mapping and extracting interacting pairs from 3D genomics data, including Hi-C, Micro-C, and derivant protocols. Microcket utilizes a unique read-stitch strategy that takes advantage of the long read cycles in modern DNA sequencers; benchmark evaluations reveal that Microcket runs much faster than the current tools along with improved mapping efficiency, and thus shows high potential in accelerating and enhancing the biological investigations into 3D genome. Microcket is freely available at https://github.com/hellosunking/Microcket .

Identifiants

DOI: 10.1038/s42003-024-06382-4 PMID: 38824179
pubmed: 38824179
doi: 10.1038/s42003-024-06382-4
pii: 10.1038/s42003-024-06382-4
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

675

Subventions

Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 82101763
Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 32270587, 32100673

Informations de copyright

© 2024. The Author(s).

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Auteurs

Yu Zhao (Y)

Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China.

Mengqi Yang (M)

Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
Department of Chemical and Biological Engineering, Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, 999077, China.

Fanglei Gong (F)

Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China.

Yuqi Pan (Y)

Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.

Minghui Hu (M)

Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China.

Qin Peng (Q)

Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518132, China.

Leina Lu (L)

Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.

Xiaowen Lyu (X)

State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Reproductive Health Research, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, 361102, China.
ORCID: 0000-0002-8317-1141

Kun Sun (K)

Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China. sunkun@szbl.ac.cn.
ORCID: 0000-0002-9883-1616

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Classifications MeSH

questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › Accelerating 3D genomics data analysis with Microcket.
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › Accelerating 3D genomics data analysis with Microcket.
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › Accelerating 3D genomics data analysis with Microcket.
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Accelerating 3D genomics data analysis with Microcket.
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Accelerating 3D genomics data analysis with Microcket.
questionsmedicales.fr › Disciplines des sciences naturelles › Mathématiques › Analyse de données › Accelerating 3D genomics data analysis with Microcket.