GBC: a parallel toolkit based on highly addressable byte-encoding blocks for extremely large-scale genotypes of species

Whole -genome sequencing projects of millions of subjects contain enormous genotypes, entailing a huge memory burden and time for computation. Here, we present GBC, a toolkit for rapidly compressing large-scale genotypes into highly addressable byte-encoding blocks under an optimized parallel framew...

Ausführliche Beschreibung

Gespeichert in:

Bibliographische Detailangaben
Veröffentlicht in:	Genome Biology Jg. 24; H. 1; S. 76
Hauptverfasser:	Zhang, Liubin, Yuan, Yangyang, Peng, Wenjie, Tang, Bin, Li, Mulin Jun, Gui, Hongsheng, Wang, Qiang, Li, Miaoxin
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	London BioMed Central 17.04.2023 Springer Nature B.V BMC
Schlagworte:	Algorithms Animal Genetics and Genomics Bioinformatics Biomedical and Life Sciences Byte-encoding genotypes Chromosomes Compression Data Compression - methods Datasets Design Evolutionary Biology genome Genomes Genomics Genomics - methods Genotype Genotype & phenotype Genotype compression Genotype management Genotypes Highly addressable genotype blocks Human Genetics Humans Large-scale genotypes Life Sciences Localization memory Method Microbial Genetics and Genomics Parallelization algorithm Plant Genetics and Genomics Software species Whole genome sequencing Parallelization algorithm Cloud computation Genotype compression Highly addressable genotype blocks Genotype management Byte-encoding genotypes Large-scale genotypes
ISSN:	1474-760X, 1474-7596, 1474-760X
Online-Zugang:	Volltext
Tags:	Tag hinzufügen Keine Tags, Fügen Sie den ersten Tag hinzu!

Abstract	Whole -genome sequencing projects of millions of subjects contain enormous genotypes, entailing a huge memory burden and time for computation. Here, we present GBC, a toolkit for rapidly compressing large-scale genotypes into highly addressable byte-encoding blocks under an optimized parallel framework. We demonstrate that GBC is up to 1000 times faster than state-of-the-art methods to access and manage compressed large-scale genotypes while maintaining a competitive compression ratio. We also showed that conventional analysis would be substantially sped up if built on GBC to access genotypes of a large population. GBC’s data structure and algorithms are valuable for accelerating large-scale genomic research.
AbstractList	Whole -genome sequencing projects of millions of subjects contain enormous genotypes, entailing a huge memory burden and time for computation. Here, we present GBC, a toolkit for rapidly compressing large-scale genotypes into highly addressable byte-encoding blocks under an optimized parallel framework. We demonstrate that GBC is up to 1000 times faster than state-of-the-art methods to access and manage compressed large-scale genotypes while maintaining a competitive compression ratio. We also showed that conventional analysis would be substantially sped up if built on GBC to access genotypes of a large population. GBC’s data structure and algorithms are valuable for accelerating large-scale genomic research. Abstract Whole -genome sequencing projects of millions of subjects contain enormous genotypes, entailing a huge memory burden and time for computation. Here, we present GBC, a toolkit for rapidly compressing large-scale genotypes into highly addressable byte-encoding blocks under an optimized parallel framework. We demonstrate that GBC is up to 1000 times faster than state-of-the-art methods to access and manage compressed large-scale genotypes while maintaining a competitive compression ratio. We also showed that conventional analysis would be substantially sped up if built on GBC to access genotypes of a large population. GBC’s data structure and algorithms are valuable for accelerating large-scale genomic research. Whole -genome sequencing projects of millions of subjects contain enormous genotypes, entailing a huge memory burden and time for computation. Here, we present GBC, a toolkit for rapidly compressing large-scale genotypes into highly addressable byte-encoding blocks under an optimized parallel framework. We demonstrate that GBC is up to 1000 times faster than state-of-the-art methods to access and manage compressed large-scale genotypes while maintaining a competitive compression ratio. We also showed that conventional analysis would be substantially sped up if built on GBC to access genotypes of a large population. GBC’s data structure and algorithms are valuable for accelerating large-scale genomic research. Whole -genome sequencing projects of millions of subjects contain enormous genotypes, entailing a huge memory burden and time for computation. Here, we present GBC, a toolkit for rapidly compressing large-scale genotypes into highly addressable byte-encoding blocks under an optimized parallel framework. We demonstrate that GBC is up to 1000 times faster than state-of-the-art methods to access and manage compressed large-scale genotypes while maintaining a competitive compression ratio. We also showed that conventional analysis would be substantially sped up if built on GBC to access genotypes of a large population. GBC's data structure and algorithms are valuable for accelerating large-scale genomic research.Whole -genome sequencing projects of millions of subjects contain enormous genotypes, entailing a huge memory burden and time for computation. Here, we present GBC, a toolkit for rapidly compressing large-scale genotypes into highly addressable byte-encoding blocks under an optimized parallel framework. We demonstrate that GBC is up to 1000 times faster than state-of-the-art methods to access and manage compressed large-scale genotypes while maintaining a competitive compression ratio. We also showed that conventional analysis would be substantially sped up if built on GBC to access genotypes of a large population. GBC's data structure and algorithms are valuable for accelerating large-scale genomic research.
ArticleNumber	76
Author	Peng, Wenjie Li, Mulin Jun Yuan, Yangyang Li, Miaoxin Wang, Qiang Zhang, Liubin Gui, Hongsheng Tang, Bin
Author_xml	– sequence: 1 givenname: Liubin surname: Zhang fullname: Zhang, Liubin organization: Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-Sen University, Center for Precision Medicine, Sun Yat-Sen University, Center for Disease Genome Research, Sun Yat-Sen University – sequence: 2 givenname: Yangyang surname: Yuan fullname: Yuan, Yangyang organization: Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-Sen University, Center for Precision Medicine, Sun Yat-Sen University, Center for Disease Genome Research, Sun Yat-Sen University, School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University – sequence: 3 givenname: Wenjie surname: Peng fullname: Peng, Wenjie organization: Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-Sen University, Center for Precision Medicine, Sun Yat-Sen University, Center for Disease Genome Research, Sun Yat-Sen University – sequence: 4 givenname: Bin surname: Tang fullname: Tang, Bin organization: Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-Sen University, Center for Precision Medicine, Sun Yat-Sen University, Center for Disease Genome Research, Sun Yat-Sen University – sequence: 5 givenname: Mulin Jun surname: Li fullname: Li, Mulin Jun organization: The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University – sequence: 6 givenname: Hongsheng surname: Gui fullname: Gui, Hongsheng organization: Behavioral Health Services, Henry Ford Health, Center for Health Policy & Health Services Research, Henry Ford Health – sequence: 7 givenname: Qiang surname: Wang fullname: Wang, Qiang organization: Mental Health Center, West China Hospital, Sichuan University – sequence: 8 givenname: Miaoxin orcidid: 0000-0002-4733-0109 surname: Li fullname: Li, Miaoxin email: limiaoxin@mail.sysu.edu.cn organization: Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-Sen University, Center for Precision Medicine, Sun Yat-Sen University, Center for Disease Genome Research, Sun Yat-Sen University, Key Laboratory of Tropical Disease Control (SYSU), Ministry of Education, Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/37069653$$D View this record in MEDLINE/PubMed
BookMark	eNqFkk9v1DAQxSNURP_AF-CALHHhErBjx0m4IFhBqVSJC0jcrIkzznrrjRfbC2w_Pd6mlLaHcrA88vze82j0jouDyU9YFM8Zfc1YK99ExmndlbTi-XRUlpePiiMmGlE2kn4_uFUfFscxrihlnajkk-KQN1R2suZHxa_TD4u3BMgGAjiHjiTv3YVNpIeIA_ETWdpx6XYEhiFgjNA7JP0uYYmT9oOdRtI7ry8iMT4Q_J0CrjHjDsKIZdSQ8REnn3YbjMQbEjeoLcanxWMDLuKz6_uk-Pbp49fF5_L8y-nZ4v15qRvapRIbyfkwNKaCWkDXioY2QDWIGjtDedO3tWHATd1LNFUNueaZYJ2sKpab_KQ4m30HDyu1CXYNYac8WHX14MOoICSrHapBGGl4jxygF73uQSAdkJmmFbISgmWvd7PXZtuvcdA4pby0O6Z3O5NdqtH_VIwy2taMZodX1w7B_9hiTGpto0bnYEK_jYqzmle0lk33X7RqadW2NW33c728h678Nkx5rXuKU0EZE5l6cXv6m7H_ZiED1Qzo4GMMaG4QRtU-cGoOnMqBU1eBU5dZ1N4TaZsgWb_fgHUPS_ksjfmfacTwb-wHVH8AUeLr1A
CitedBy_id	crossref_primary_10_1093_gigascience_giae046
Cites_doi	10.1038/nature15393 10.1111/1755-0998.13438 10.1093/bioinformatics/bty875 10.1086/519795 10.1093/gigascience/giab008 10.1093/bioinformatics/btr330 10.1093/bioinformatics/btaa290 10.1093/bioinformatics/bty023 10.1016/j.cell.2019.09.019 10.5281/zenodo.7737556 10.1038/s41586-018-0579-z 10.1093/bioinformatics/btz508 10.1016/j.xgen.2021.100029 10.1093/bioinformatics/btw437 10.1038/nmeth.3654 10.1126/science.356262 10.1093/bioinformatics/btx145 10.1093/bioinformatics/btt460 10.1101/2020.12.18.423437 10.1093/bioinformatics/btv613 10.1093/bioinformatics/btu014 10.1038/s41586-021-03205-y
ContentType	Journal Article
Copyright	The Author(s) 2023 2023. The Author(s). 2023. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
Copyright_xml	– notice: The Author(s) 2023 – notice: 2023. The Author(s). – notice: 2023. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
DBID	C6C AAYXX CITATION CGR CUY CVF ECM EIF NPM 3V. 7X7 7XB 88E 8FE 8FH 8FI 8FJ 8FK ABUWG AFKRA AZQEC BBNVY BENPR BHPHI CCPQU DWQXO FYUFA GHDGH GNUQQ HCIFZ K9. LK8 M0S M1P M7P PHGZM PHGZT PIMPY PJZUB PKEHL PPXIY PQEST PQGLB PQQKQ PQUKI PRINS 7X8 7S9 L.6 5PM DOA
DOI	10.1186/s13059-023-02906-z
DatabaseName	Springer Nature OA Free Journals CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed ProQuest Central (Corporate) Health & Medical Collection ProQuest Central (purchase pre-March 2016) Medical Database (Alumni Edition) ProQuest SciTech Collection ProQuest Natural Science Collection Hospital Premium Collection Hospital Premium Collection (Alumni Edition) ProQuest Central (Alumni) (purchase pre-March 2016) ProQuest Central (Alumni) ProQuest Central UK/Ireland ProQuest Central Essentials Biological Science Collection ProQuest Central Natural Science Collection ProQuest One ProQuest Central Proquest Health Research Premium Collection Health Research Premium Collection (Alumni) ProQuest Central Student SciTech Premium Collection ProQuest Health & Medical Complete (Alumni) ProQuest Biological Science Collection ProQuest Health & Medical Collection Medical Database Biological Science Database ProQuest Central Premium ProQuest One Academic (New) Publicly Available Content Database ProQuest Health & Medical Research Collection ProQuest One Academic Middle East (New) ProQuest One Health & Nursing ProQuest One Academic Eastern Edition (DO NOT USE) ProQuest One Applied & Life Sciences ProQuest One Academic (retired) ProQuest One Academic UKI Edition ProQuest Central China MEDLINE - Academic AGRICOLA AGRICOLA - Academic PubMed Central (Full Participant titles) DOAJ Directory of Open Access Journals
DatabaseTitle	CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) Publicly Available Content Database ProQuest Central Student ProQuest One Academic Middle East (New) ProQuest Central Essentials ProQuest Health & Medical Complete (Alumni) ProQuest Central (Alumni Edition) SciTech Premium Collection ProQuest One Community College ProQuest One Health & Nursing ProQuest Natural Science Collection ProQuest Central China ProQuest Central ProQuest One Applied & Life Sciences ProQuest Health & Medical Research Collection Health Research Premium Collection Health and Medicine Complete (Alumni Edition) Natural Science Collection ProQuest Central Korea Health & Medical Research Collection Biological Science Collection ProQuest Central (New) ProQuest Medical Library (Alumni) ProQuest Biological Science Collection ProQuest One Academic Eastern Edition ProQuest Hospital Collection Health Research Premium Collection (Alumni) Biological Science Database ProQuest SciTech Collection ProQuest Hospital Collection (Alumni) ProQuest Health & Medical Complete ProQuest Medical Library ProQuest One Academic UKI Edition ProQuest One Academic ProQuest One Academic (New) ProQuest Central (Alumni) MEDLINE - Academic AGRICOLA AGRICOLA - Academic
DatabaseTitleList	CrossRef Publicly Available Content Database MEDLINE AGRICOLA MEDLINE - Academic
Database_xml	– sequence: 1 dbid: DOA name: DOAJ Directory of Open Access Journals url: https://www.doaj.org/ sourceTypes: Open Website – sequence: 2 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 3 dbid: PIMPY name: Publicly Available Content Database url: http://search.proquest.com/publiccontent sourceTypes: Aggregation Database
DeliveryMethod	fulltext_linktorsrc
Discipline	Biology
EISSN	1474-760X
EndPage	76
ExternalDocumentID	oai_doaj_org_article_d4f6f3be3aab4bcba4e0de1f78462441 PMC10108510 37069653 10_1186_s13059_023_02906_z
Genre	Research Support, Non-U.S. Gov't Journal Article
GrantInformation_xml	– fundername: National Natural Science Foundation of China grantid: 31771401; 31970650 funderid: http://dx.doi.org/10.13039/501100001809 – fundername: ; grantid: 31771401; 31970650
GroupedDBID	--- 0R~ 29H 4.4 53G 5GY 5VS 7X7 88E 8FE 8FH 8FI 8FJ AAFWJ AAHBH AAJSJ AASML ABUWG ACGFO ACGFS ACJQM ACPRK ADBBV ADUKV AEGXH AFKRA AFPKN AHBYD AIAGR ALMA_UNASSIGNED_HOLDINGS AMKLP AMTXH AOIAM AOIJS BAPOH BAWUL BBNVY BCNDV BENPR BFQNJ BHPHI BMC BPHCQ BVXVI C6C CCPQU EBD EBLON EBS EMOBN FYUFA GROUPED_DOAJ GX1 HCIFZ HMCUK IAO IGS IHR ISR ITC KPI LK8 M1P M7P PHGZM PHGZT PIMPY PJZUB PPXIY PQGLB PQQKQ PROAC PSQYO PUEGO ROL RPM RSV SJN SOJ SV3 UKHRP AAYXX AFFHD CITATION 3V. ACRMQ ADINQ ALIPV C24 CGR CUY CVF ECM EIF NPM 7XB 8FK AZQEC DWQXO GNUQQ K9. PKEHL PQEST PQUKI PRINS 7X8 7S9 L.6 5PM
ID	FETCH-LOGICAL-c709t-e7633dd7f2a54a984707a0ca45e9f037b85f1a3f5b6ef25a1a3307a196221b853
IEDL.DBID	DOA
ISICitedReferencesCount	2
ISICitedReferencesURI	http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000984385600004&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
ISSN	1474-760X 1474-7596
IngestDate	Mon Nov 10 04:24:32 EST 2025 Tue Nov 04 02:06:44 EST 2025 Fri Sep 05 15:04:34 EDT 2025 Fri Sep 05 07:43:54 EDT 2025 Tue Oct 14 14:10:33 EDT 2025 Thu Jan 02 22:53:16 EST 2025 Sat Nov 29 04:56:03 EST 2025 Tue Nov 18 22:49:34 EST 2025 Sat Sep 06 07:17:32 EDT 2025
IsDoiOpenAccess	true
IsOpenAccess	true
IsPeerReviewed	true
IsScholarly	true
Issue	1
Keywords	Parallelization algorithm Cloud computation Genotype compression Highly addressable genotype blocks Genotype management Byte-encoding genotypes Large-scale genotypes
Language	English
License	2023. The Author(s). Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
LinkModel	DirectLink
MergedId	FETCHMERGED-LOGICAL-c709t-e7633dd7f2a54a984707a0ca45e9f037b85f1a3f5b6ef25a1a3307a196221b853
Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23
ORCID	0000-0002-4733-0109
OpenAccessLink	https://doaj.org/article/d4f6f3be3aab4bcba4e0de1f78462441
PMID	37069653
PQID	2803040114
PQPubID	2040232
PageCount	1
ParticipantIDs	doaj_primary_oai_doaj_org_article_d4f6f3be3aab4bcba4e0de1f78462441 pubmedcentral_primary_oai_pubmedcentral_nih_gov_10108510 proquest_miscellaneous_3153205679 proquest_miscellaneous_2802885081 proquest_journals_2803040114 pubmed_primary_37069653 crossref_primary_10_1186_s13059_023_02906_z crossref_citationtrail_10_1186_s13059_023_02906_z springer_journals_10_1186_s13059_023_02906_z
PublicationCentury	2000
PublicationDate	2023-04-17
PublicationDateYYYYMMDD	2023-04-17
PublicationDate_xml	– month: 04 year: 2023 text: 2023-04-17 day: 17
PublicationDecade	2020
PublicationPlace	London
PublicationPlace_xml	– name: London – name: England
PublicationTitle	Genome Biology
PublicationTitleAbbrev	Genome Biol
PublicationTitleAlternate	Genome Biol
PublicationYear	2023
Publisher	BioMed Central Springer Nature B.V BMC
Publisher_xml	– name: BioMed Central – name: Springer Nature B.V – name: BMC
References	RM Layer (2906_CR11) 2016; 13 D Lan (2906_CR6) 2020; 36 A Danek (2906_CR12) 2018; 34 S Deorowicz (2906_CR5) 2019; 35 D Taliun (2906_CR18) 2021; 590 R Durbin (2906_CR9) 2014; 30 2906_CR24 S Deorowicz (2906_CR4) 2013; 29 C Zhang (2906_CR16) 2019; 35 A Auton (2906_CR21) 2015; 526 2906_CR20 C Bycroft (2906_CR3) 2018; 562 D Wu (2906_CR14) 2019; 179 HL Rehm (2906_CR13) 2021; 1 P Danecek (2906_CR1) 2011; 27 X Zheng (2906_CR22) 2017; 33 M Li (2906_CR15) 2017; 45 C Theodoris (2906_CR17) 2021; 21 S Purcell (2906_CR2) 2007; 81 P Menozzi (2906_CR19) 1978; 201 2906_CR7 P Danecek (2906_CR8) 2021; 10 K Tatwawadi (2906_CR23) 2016; 32 H Li (2906_CR10) 2016; 32
References_xml	– volume: 526 start-page: 68 issue: 7571 year: 2015 ident: 2906_CR21 publication-title: Nature doi: 10.1038/nature15393 – volume: 21 start-page: 2580 issue: 7 year: 2021 ident: 2906_CR17 publication-title: Mol Ecol Resour doi: 10.1111/1755-0998.13438 – volume: 35 start-page: 1786 issue: 10 year: 2019 ident: 2906_CR16 publication-title: Bioinformatics doi: 10.1093/bioinformatics/bty875 – volume: 81 start-page: 559 issue: 3 year: 2007 ident: 2906_CR2 publication-title: Am J Hum Genet doi: 10.1086/519795 – volume: 10 start-page: giab008 issue: 2 year: 2021 ident: 2906_CR8 publication-title: Gigascience doi: 10.1093/gigascience/giab008 – volume: 27 start-page: 2156 issue: 15 year: 2011 ident: 2906_CR1 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr330 – volume: 36 start-page: 4091 issue: 13 year: 2020 ident: 2906_CR6 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btaa290 – volume: 34 start-page: 1834 issue: 11 year: 2018 ident: 2906_CR12 publication-title: Bioinformatics doi: 10.1093/bioinformatics/bty023 – volume: 179 start-page: 736 issue: 3 year: 2019 ident: 2906_CR14 publication-title: Cell doi: 10.1016/j.cell.2019.09.019 – ident: 2906_CR24 doi: 10.5281/zenodo.7737556 – volume: 562 start-page: 203 issue: 7726 year: 2018 ident: 2906_CR3 publication-title: Nature doi: 10.1038/s41586-018-0579-z – volume: 35 start-page: 4791 issue: 22 year: 2019 ident: 2906_CR5 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btz508 – volume: 1 start-page: 100029 issue: 2 year: 2021 ident: 2906_CR13 publication-title: Cell Genom doi: 10.1016/j.xgen.2021.100029 – volume: 32 start-page: i479 issue: 17 year: 2016 ident: 2906_CR23 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btw437 – volume: 13 start-page: 63 issue: 1 year: 2016 ident: 2906_CR11 publication-title: Nat Methods doi: 10.1038/nmeth.3654 – volume: 201 start-page: 786 issue: 4358 year: 1978 ident: 2906_CR19 publication-title: Science doi: 10.1126/science.356262 – volume: 33 start-page: 2251 issue: 15 year: 2017 ident: 2906_CR22 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btx145 – volume: 29 start-page: 2572 issue: 20 year: 2013 ident: 2906_CR4 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btt460 – ident: 2906_CR7 doi: 10.1101/2020.12.18.423437 – volume: 32 start-page: 590 issue: 4 year: 2016 ident: 2906_CR10 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv613 – volume: 45 start-page: e75 issue: 9 year: 2017 ident: 2906_CR15 publication-title: Nucleic Acids Res – ident: 2906_CR20 – volume: 30 start-page: 1266 issue: 9 year: 2014 ident: 2906_CR9 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu014 – volume: 590 start-page: 290 issue: 7845 year: 2021 ident: 2906_CR18 publication-title: Nature doi: 10.1038/s41586-021-03205-y
SSID	ssj0019426 ssj0017866
Score	2.4325047
Snippet	Whole -genome sequencing projects of millions of subjects contain enormous genotypes, entailing a huge memory burden and time for computation. Here, we present... Whole -genome sequencing projects of millions of subjects contain enormous genotypes, entailing a huge memory burden and time for computation. Here, we present... Abstract Whole -genome sequencing projects of millions of subjects contain enormous genotypes, entailing a huge memory burden and time for computation. Here,...
SourceID	doaj pubmedcentral proquest pubmed crossref springer
SourceType	Open Website Open Access Repository Aggregation Database Index Database Enrichment Source Publisher
StartPage	76
SubjectTerms	Algorithms Animal Genetics and Genomics Bioinformatics Biomedical and Life Sciences Byte-encoding genotypes Chromosomes Compression Data Compression - methods Datasets Design Evolutionary Biology genome Genomes Genomics Genomics - methods Genotype Genotype & phenotype Genotype compression Genotype management Genotypes Highly addressable genotype blocks Human Genetics Humans Large-scale genotypes Life Sciences Localization memory Method Microbial Genetics and Genomics Parallelization algorithm Plant Genetics and Genomics Software species Whole genome sequencing
SummonAdditionalLinks	– databaseName: Health & Medical Collection dbid: 7X7 link: http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV1Lb9QwELaggMSF9yNQkJG4QVQnTuyYC6IVhVPFAaS9WbZj01WjpGxS0PbXM-MkWy3QXjistLueleKdme-b8WOGkNcGSLgKkORY6X1a-OhSVqXGWwfgGJg1Y7MJeXRULRbqy7Tg1k_HKmdMjEBddw7XyPewixIYHITv709_pNg1CndXpxYa18kNbJuNdi4Xm4QrkxXGKtMHVeTjVSM8gFgqMd-gqcReD0BeqhToC14KUuzzLZaKxfz_FYH-fZDyj93USFKHd_93evfInSk8pR9Ge7pPrvn2Abk1NqxcPyS_Pu0fvKOGYsHwpvENHbquOVkOFMmwpl1Lsfxxs6aAZ7G5im08tevBp1gvE2mSWmDPk55CrEyBF3B1EsQbPI-e9mAvnmLVWFwY7mkXKF4EhVz-Efl2-PHrwed0at2QOsnUkHqALV7XMuSmLIwCCmTSMGeK0qvAuLRVGTLDQ2mFD3lp4D2AjQE4yPMMBvljstN2rX9KqJCWuawWzDJfKMYs8GduaiHKXDjHXUKyWVXaTXXNsb1Go2N-Uwk9qleDenVUrz5PyJvNb07Hqh5XSu-jBWwksSJ3_KJbfdeTg-u6CCJw67kxtrDOmsKz2mdBQoAHIVSWkN1Z8XqCiV5faD0hrzbD4OC4a2Na351FmbyqII7OLpfhGfb3KIVUCXkymuTmablkQomSJ6TaMtat6WyPtMvjWGgc4BojcpaQt7NdXzz75f_Xs6un-pzczqOrFWkmd8nOsDrzL8hN93NY9quX0YN_A3ygS4A priority: 102 providerName: ProQuest – databaseName: Springer Journals dbid: RSV link: http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1Jb9UwEB5BAYkL-xIoyEjcIMJZbMfcaEXhVCGxqDfLduzy1ChBLyno9dczdhb0oEWCQ6QonkiOMzPfjJdvAJ5rBOHKY5JjhHNp6aJJGZlqZyw6R0-NHotNiMPD6uhIfpgOhfXzbvd5STJ66mjWFX_Vo7dlMkWMwUtiHnx2Ga6wwDYTcvSPX5a1A4mgMx-POfe9LQiKTP3nhZd_7pL8bak0ItDBzf_r-y24MUWc5M2oIrfhkmvvwLWxBuXmLvx4t7f_mmgSOMCbxjVk6LrmZDWQgG816VoSGI2bDUEXFeulmMYRsxlcGigwA_IRg4B40hMMfwm6-jDhiOJN2GKe9qgCjgQi2DDX25POk3C2E9Pze_D54O2n_ffpVI0htYLKIXXoiYq6Fj7XrNQSUY0KTa0umZOeFsJUzGe68Mxw53Om8R79h0YLz_MMG4v7sNN2rXsIhAtDbVZzaqgrJaUGITHXNecs59YWNoFs_kHKTlTloWJGo2LKUnE1DqjCAVVxQNVZAi-Wd76NRB1_ld4L_32RDCTb8UG3PlaTzaq69NwXxhVam9JYo0tHa5d5gTEbRkVZAruz1qjJ8nsVqn2hY8Q0M4FnSzPabFiI0a3rTqNMXlUYGmcXyxRZKNnBuJAJPBgVceltISiXnBUJVFsquvU52y3t6mvkDkcPHIJsmsDLWVN_9f3i8Xr0b-KP4Xoelb1MM7ELO8P61D2Bq_b7sOrXT6O5_gRgQT4B priority: 102 providerName: Springer Nature
Title	GBC: a parallel toolkit based on highly addressable byte-encoding blocks for extremely large-scale genotypes of species
URI	https://link.springer.com/article/10.1186/s13059-023-02906-z https://www.ncbi.nlm.nih.gov/pubmed/37069653 https://www.proquest.com/docview/2803040114 https://www.proquest.com/docview/2802885081 https://www.proquest.com/docview/3153205679 https://pubmed.ncbi.nlm.nih.gov/PMC10108510 https://doaj.org/article/d4f6f3be3aab4bcba4e0de1f78462441
Volume	24
WOSCitedRecordID	wos000984385600004&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
hasFullText	1
inHoldings	1
isFullTextHit
isPrint
journalDatabaseRights	– providerCode: PRVADU databaseName: BioMedCentral customDbUrl: eissn: 1474-760X dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017866 issn: 1474-760X databaseCode: RBZ dateStart: 20000101 isFulltext: true titleUrlDefault: https://www.biomedcentral.com/search/ providerName: BioMedCentral – providerCode: PRVAON databaseName: DOAJ Directory of Open Access Journals customDbUrl: eissn: 1474-760X dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0019426 issn: 1474-760X databaseCode: DOA dateStart: 20000101 isFulltext: true titleUrlDefault: https://www.doaj.org/ providerName: Directory of Open Access Journals – providerCode: PRVPQU databaseName: Biological Science Database customDbUrl: eissn: 1474-760X dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0019426 issn: 1474-760X databaseCode: M7P dateStart: 20150101 isFulltext: true titleUrlDefault: http://search.proquest.com/biologicalscijournals providerName: ProQuest – providerCode: PRVPQU databaseName: Health & Medical Collection customDbUrl: eissn: 1474-760X dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0019426 issn: 1474-760X databaseCode: 7X7 dateStart: 20150101 isFulltext: true titleUrlDefault: https://search.proquest.com/healthcomplete providerName: ProQuest – providerCode: PRVPQU databaseName: ProQuest Central customDbUrl: eissn: 1474-760X dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0019426 issn: 1474-760X databaseCode: BENPR dateStart: 20150101 isFulltext: true titleUrlDefault: https://www.proquest.com/central providerName: ProQuest – providerCode: PRVPQU databaseName: Publicly Available Content Database customDbUrl: eissn: 1474-760X dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0019426 issn: 1474-760X databaseCode: PIMPY dateStart: 20150101 isFulltext: true titleUrlDefault: http://search.proquest.com/publiccontent providerName: ProQuest – providerCode: PRVAVX databaseName: Springer Journals customDbUrl: eissn: 1474-760X dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0019426 issn: 1474-760X databaseCode: RSV dateStart: 20000201 isFulltext: true titleUrlDefault: https://link.springer.com/search?facet-content-type=%22Journal%22 providerName: Springer Nature
link	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV1Lb9QwEB5BAYkL4lkCZWUkbhDVedkxN7ZqgQOrqDy0cIlsxxarRglqUtD21zN2koUFChcOibKxI3k9j28mdr4BeCIRhHOLSY7ixoSp8SalRCiN0ugcLVVyKDbBF4t8uRTFT6W-3J6wgR54mLj9KrXMJsokUqpUaSVTQysTWY7AidDkEx_KxZRMjesHAoFn-kQmZ_sdeupMhIhPeAjMoc-3YMiz9f8pxPx9p-Qvy6UehY5uwo0xfCQvhmHfgkumuQ3XhoKS6zvw7eX84DmRxBF617WpSd-29cmqJw6sKtI2xNET12uC_sYXP1G1IWrdm9DxWToYIwrR7aQjGMsS9Nvu7SF2r91-8bBDeRriWF3di9uOtJa4DzUx174L748O3x28CsfSCqHmVPShQbeSVBW3scxSKRCiKJdUyzQzwtKEqzyzkUxsppixcSbxGp2BRHON4wgbk3uw07SNuQ-EcUV1VDGqqEkFpQrxLZYVY1nMtE50ANE006Ueecdd-Yu69PlHzspBOiVKp_TSKc8DeLp55svAuvHX3nMnwE1Px5jtb6AelaMelf_SowD2JvGXoxl3pSvdhV4Oc8YAHm-a0QDdqopsTHvm-8R5jnFudHGfJHL1NzLGRQC7g0ZtRptwygTLkgDyLV3b-jvbLc3qsycCR3fqImYawLNJLX-M_eL5evA_5ushXI-9PaVhxPdgpz89M4_gqv7ar7rTGVzmS-7P-QyuzA8XxfHMW-jMba4t8F7x-k3xEX8dzz-589sP3wHJxELB
linkProvider	Directory of Open Access Journals
linkToHtml	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw1V1Jb9NAFH4qKQgu7IuhwCDBCayOtxkPEkK0UBq1jXooUnsyM_YYolp2iVOq9EfxG3nPS6oA7a0HDpGSzMTyON_3llneB_BSoxOOc0xyjLTWDW1DKaNcbU2KxjHnRrdiE3I0ivf31e4S_OrPwtC2yt4mNoY6q1KaI18lFSUEHIbv749-uKQaRaurvYRGC4stOzvBlK1-N_yI_-8r39_4tLe-6XaqAm4quZq6FhkVZJnMfR2FWqF15lLzVIeRVTkPpImj3NNBHhlhcz_S-B55oBGpvu9hY4DXvQLLIYKdD2B5d7izezBft5AxRUfdBxX67eEm2vIYKdGf2YnFao2uI1IuOkx8KUzqTxf8YiMf8K-Y9--tm3-s3zZucePW__ZAb8PNLgBnH1rG3IElW96Fa60k5-wenHxeW3_LNKOS6EVhCzatquJwPGXk7jNWlYwKPBczhha7kY8xhWVmNrUuVQSlQIAZjA8Oa4bZAEPPR_Ov2L2gHfdujYywjOri0tR3zaqc0VHXsa3vw5dLGfUDGJRVaR8BE9Lw1MsEN9yGinODEYKvMyEiX6RpkDrg9dBI0q5yOwmIFEmTwcUiaeGUIJySBk7JqQOv5785auuWXNh7jRA370k1x5svqsm3pDNhSRbmIg-MDbQ2oUmNDi3PrJdLDGExSPQcWOmBlnSGsE7OUObAi3kzmjBal9KlrY6bPn4cY6bgnd8n8EjBJBJSOfCwpcD8bgPJhRJR4EC8QI6F4Sy2lOPvTSl1dEiUc3AH3vQ8Orv385_X44uH-hyub-7tbCfbw9HWE7jhNzQPXU-uwGA6ObZP4Wr6czquJ886-8Hg62Uz7DfoZ6h-
linkToPdf	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV1Zb9QwEB5BOcQLNyVQwEi8QVTnsmPeaGEBgVYVl_pm2YlNV42SapOCtr-esXPAQouEeIgUxWPJcWbmm4ntbwCeKATh3GKSo7kxYWq8SWkRKqMLdI6WatUXm-Dzeb6_L_Z-OcXvd7uPS5L9mQbH0lR320el7U08Z9stet5MhIg3eAnMiU_Ow4UUMxm3qevDxy_TOoJAABqPypzabw2OPGv_aaHmnzsmf1s29Wg0u_b_73Edrg6RKHnRq84NOGfqm3Cpr025ugXfX-_sPieKOG7wqjIV6ZqmOlx0xOFeSZqaOKbjakXQdfk6KroyRK86EzpqTIeIRCNQHrYEw2KCEOB-RKJ45baehy2qhiGOINb9A25JY4k784lp-234PHv1afdNOFRpCAtORRca9FBJWXIbqyxVAtGOckULlWZGWJpwnWc2UonNNDM2zhTeo19RaPlxHGFjcgc26qY2d4EwrmkRlYxqalJBqUaojFXJWBazokiKAKLxY8lioDB3lTQq6VOZnMl-QiVOqPQTKk8CeDr1OeoJPP4qveN0YJJ05Nv-QbP8KgdblmVqmU20SZTSqS60Sg0tTWQ5xnIYLUUBbI0aJAeP0EpXBQwdJqafATyemtGW3QKNqk1z7GXiPMeQOTpbJolcKY-McRHAZq-U02gTTplgWRJAvqaua6-z3lIvDjynOHpmF3zTAJ6NWvtz7GfP171_E38El_dezuT7t_N39-FK7PU-DSO-BRvd8tg8gIvFt27RLh96K_4BXs9JyQ
openUrl	ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=GBC%3A+a+parallel+toolkit+based+on+highly+addressable+byte-encoding+blocks+for+extremely+large-scale+genotypes+of+species&rft.jtitle=Genome+biology&rft.au=Liubin+Zhang&rft.au=Yangyang+Yuan&rft.au=Wenjie+Peng&rft.au=Bin+Tang&rft.date=2023-04-17&rft.pub=BMC&rft.eissn=1474-760X&rft.volume=24&rft.issue=1&rft.spage=1&rft.epage=22&rft_id=info:doi/10.1186%2Fs13059-023-02906-z&rft.externalDBID=DOA&rft.externalDocID=oai_doaj_org_article_d4f6f3be3aab4bcba4e0de1f78462441
thumbnail_l	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1474-760X&client=summon
thumbnail_m	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1474-760X&client=summon
thumbnail_s	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1474-760X&client=summon