Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies.
Journal
Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192
Informations de publication
Date de publication:
26 11 2019
26 11 2019
Historique:
received:
07
01
2019
accepted:
31
10
2019
entrez:
28
11
2019
pubmed:
28
11
2019
medline:
21
10
2020
Statut:
epublish
Résumé
Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2-7.2 Mbp, 40-73% GC content, and 1.5-7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel.
Identifiants
pubmed: 31772173
doi: 10.1038/s41597-019-0287-z
pii: 10.1038/s41597-019-0287-z
pmc: PMC6879543
doi:
Types de publication
Dataset
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
285Subventions
Organisme : DOE | Office of Science (SC)
ID : DE-AC02-05CH11231
Pays : International
Références
PLoS One. 2017 Oct 26;12(10):e0185056
pubmed: 29073143
Sci Rep. 2018 May 29;8(1):8286
pubmed: 29844487
J Clin Microbiol. 2017 May;55(5):1285-1298
pubmed: 28275074
Biomol Detect Quantif. 2015 Mar;3:1-8
pubmed: 26753127
Proc Natl Acad Sci U S A. 1996 Nov 26;93(24):13770-3
pubmed: 8943010
J Clin Microbiol. 2017 Dec;55(12):3530-3543
pubmed: 29021151
Genome Res. 2018 Feb;28(2):266-274
pubmed: 29273626
Sci Rep. 2017 Jul 18;7(1):5657
pubmed: 28720805
Proc Natl Acad Sci U S A. 2018 Sep 25;115(39):9726-9731
pubmed: 30201725
Nature. 2008 Nov 6;456(7218):53-9
pubmed: 18987734
Front Microbiol. 2017 Oct 31;8:2105
pubmed: 29163399
Sci Rep. 2018 Jun 29;8(1):9830
pubmed: 29959349
F1000Res. 2017 May 3;6:618
pubmed: 30135709
Nat Methods. 2008 Feb;5(2):183-8
pubmed: 18204455
PLoS One. 2016 Dec 9;11(12):e0167600
pubmed: 27936026
Sci Data. 2016 Sep 27;3:160081
pubmed: 27673566
Sci Rep. 2017 Aug 21;7(1):8345
pubmed: 28827531
Sci Rep. 2017 Jun 14;7(1):3510
pubmed: 28615658
Plant J. 2018 Nov;96(3):670-684
pubmed: 30054939
Gigascience. 2014 Oct 20;3:22
pubmed: 25386338
Elife. 2016 Apr 07;5:
pubmed: 27054412
Gigascience. 2016 Aug 02;5(1):34
pubmed: 27485345
Nat Methods. 2017 Nov;14(11):1063-1071
pubmed: 28967888
Nucleic Acids Res. 2008 Sep;36(16):e105
pubmed: 18660515
Genome Biol. 2004;5(2):R12
pubmed: 14759262
Gigascience. 2018 Apr 1;7(4):
pubmed: 29617771
Nature. 2012 Jun 13;486(7402):215-21
pubmed: 22699610
Nucleic Acids Res. 2018 Mar 16;46(5):2159-2168
pubmed: 29401301
Gigascience. 2017 Mar 1;6(3):1-10
pubmed: 28327976
PLoS One. 2013 Nov 06;8(11):e78257
pubmed: 24223144
Sci Rep. 2014 Feb 11;4:4062
pubmed: 24513580
Genome Biol. 2015 May 30;16:114
pubmed: 26025440
Appl Environ Microbiol. 2018 Jan 31;84(4):
pubmed: 29196295
PLoS One. 2018 Mar 22;13(3):e0194366
pubmed: 29566006
Sci Rep. 2017 Aug 3;7(1):7213
pubmed: 28775309
Front Microbiol. 2015 Aug 18;6:766
pubmed: 26347715
Genome Res. 2015 Nov;25(11):1750-6
pubmed: 26447147
Int J Syst Bacteriol. 1995 Oct;45(4):676-81
pubmed: 7547286
PeerJ. 2015 Nov 24;3:e1441
pubmed: 26623194
BMC Genomics. 2015 Oct 24;16:856
pubmed: 26496746
ISME J. 2016 Aug;10(8):2020-32
pubmed: 26859772
Front Microbiol. 2014 Apr 07;5:109
pubmed: 24778628
Genome Biol. 2011 Nov 08;12(11):R112
pubmed: 22067484
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
Clin Microbiol Rev. 2017 Oct;30(4):1015-1063
pubmed: 28855266
Bioinformatics. 2013 Apr 15;29(8):1072-5
pubmed: 23422339
Bioinformatics. 2015 Sep 1;31(17):2885-7
pubmed: 25953801
Nature. 2016 Feb 11;530(7589):228-232
pubmed: 26840485
Genome Biol. 2013 Jul 03;14(7):405
pubmed: 23822731
Mol Ecol Resour. 2014 Nov;14(6):1097-102
pubmed: 25187008
Nat Biotechnol. 2018 Apr;36(4):338-345
pubmed: 29431738
Sci Rep. 2016 Jun 28;6:28625
pubmed: 27350167
Curr Protoc Bioinformatics. 2014 Sep 08;47:11.12.1-34
pubmed: 25199790
Nucleic Acids Res. 2015 Dec 15;43(22):e152
pubmed: 26240383
F1000Res. 2015 Oct 15;4:1075
pubmed: 26834992
Nat Methods. 2015 Aug;12(8):733-5
pubmed: 26076426
PLoS One. 2016 Mar 03;11(3):e0150528
pubmed: 26937682
Sci Rep. 2018 May 21;8(1):7903
pubmed: 29785005
Nat Biotechnol. 2015 Mar;33(3):296-300
pubmed: 25485618
Gigascience. 2015 Mar 26;4:12
pubmed: 25815165
J Antimicrob Chemother. 2015 Oct;70(10):2775-8
pubmed: 26221019
Sci Rep. 2018 Aug 9;8(1):11907
pubmed: 30093614
Cancer Biol Ther. 2016;17(3):246-53
pubmed: 26787508