Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads.
Assembly
Benchmark
Binning
Leaderboard metagenome
Long reads
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
31 10 2019
31 10 2019
Historique:
received:
27
03
2019
accepted:
23
09
2019
entrez:
2
11
2019
pubmed:
2
11
2019
medline:
6
2
2020
Statut:
epublish
Résumé
As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach leaderboard metagenome sequencing. To explore protocol optimization for leaderboard metagenomics in real samples, we introduce a benchmark of library prep and sequencing using internal references generated by synthetic long-read technology, allowing us to evaluate high-throughput library preparation methods against gold-standard reference genomes derived from the samples themselves. We introduce a low-cost protocol for high-throughput library preparation and sequencing.
Identifiants
pubmed: 31672156
doi: 10.1186/s13059-019-1834-9
pii: 10.1186/s13059-019-1834-9
pmc: PMC6822431
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Validation Study
Langues
eng
Sous-ensembles de citation
IM
Pagination
226Subventions
Organisme : NIH HHS
ID : T32GM8806
Pays : United States
Organisme : NIDA NIH HHS
ID : DA046171
Pays : United States
Organisme : NIDA NIH HHS
ID : DA039562
Pays : United States
Références
Nat Biotechnol. 2016 Jan;34(1):64-9
pubmed: 26655498
Nat Methods. 2017 Nov;14(11):1063-1071
pubmed: 28967888
Bioinformatics. 2011 Nov 1;27(21):2957-63
pubmed: 21903629
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
PLoS One. 2013 Jun 28;8(6):e67539
pubmed: 23840736
Microbiome. 2018 Sep 15;6(1):158
pubmed: 30219103
BMC Biotechnol. 2013 Nov 20;13:104
pubmed: 24256843
Syst Biol. 2020 Nov 1;69(6):1212-1230
pubmed: 32298451
Elife. 2017 Jul 05;6:
pubmed: 28678007
PeerJ. 2019 Jul 26;7:e7359
pubmed: 31388474
Nature. 2012 Jun 13;486(7402):207-14
pubmed: 22699609
Nat Commun. 2017 Jan 27;8:13919
pubmed: 28128213
Bioinformatics. 2016 Apr 1;32(7):1009-15
pubmed: 26589280
Genome Biol. 2014;15(7):R89
pubmed: 25146375
Bioinformatics. 2018 Oct 15;34(20):3600
pubmed: 29788404
Nature. 2017 Nov 23;551(7681):457-463
pubmed: 29088705
PeerJ. 2019 Oct 11;7:e7755
pubmed: 31616586
mSystems. 2018 Nov 13;3(6):
pubmed: 30443602
ISME J. 2015 Jan;9(1):68-80
pubmed: 25012900
Gigascience. 2019 May 1;8(5):
pubmed: 31089679
Bioinformatics. 2016 Feb 15;32(4):605-7
pubmed: 26515820
Proc Natl Acad Sci U S A. 2015 Nov 10;112(45):14024-9
pubmed: 26512100
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5540-5
pubmed: 23509275
Nat Methods. 2007 Jun;4(6):495-500
pubmed: 17468765
Nat Methods. 2014 Nov;11(11):1144-6
pubmed: 25218180
Nature. 2010 Mar 4;464(7285):59-65
pubmed: 20203603
ISME J. 2017 Dec;11(12):2864-2868
pubmed: 28742071
PeerJ. 2017 Aug 30;5:e3720
pubmed: 28875074
Science. 2014 Apr 25;344(6182):416-20
pubmed: 24763590
mSystems. 2018 May 15;3(3):
pubmed: 29795809
PLoS One. 2014 Sep 04;9(9):e106689
pubmed: 25188499
ISME J. 2012 Jun;6(6):1186-99
pubmed: 22170421
Nat Biotechnol. 2019 Oct;37(10):1155-1162
pubmed: 31406327
Genome Biol. 2014 Mar 03;15(3):R46
pubmed: 24580807
Genome Biol. 2011;12(5):R50
pubmed: 21624126
PeerJ. 2016 Sep 22;4:e2486
pubmed: 27688978
Genome Res. 2017 May;27(5):824-834
pubmed: 28298430
Bioinformatics. 2016 Oct 1;32(19):3047-8
pubmed: 27312411
J Antimicrob Chemother. 2014 May;69(5):1275-81
pubmed: 24370932
mBio. 2014 Jul 15;5(4):e01371-14
pubmed: 25028427
Nat Methods. 2016 Mar;13(3):248-50
pubmed: 26828418
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
Microbiome. 2019 Apr 16;7(1):61
pubmed: 30992083
Bioinformatics. 2013 Apr 15;29(8):1072-5
pubmed: 23422339
Nat Biotechnol. 2014 Mar;32(3):261-266
pubmed: 24561555
Nature. 2019 Apr;568(7753):499-504
pubmed: 30745586
Genome Res. 2015 Jul;25(7):1043-55
pubmed: 25977477
J Lab Autom. 2016 Aug;21(4):557-67
pubmed: 26891732
Cell. 2019 Jan 24;176(3):649-662.e20
pubmed: 30661755
PLoS One. 2011;6(8):e22099
pubmed: 21850220
Bioinformatics. 2015 Mar 15;31(6):817-24
pubmed: 25388150
Genome Biol. 2019 Oct 31;20(1):226
pubmed: 31672156
Genome Res. 2013 Jan;23(1):111-20
pubmed: 22936250
Nat Biotechnol. 2014 Aug;32(8):822-8
pubmed: 24997787
Genome Res. 2012 Mar;22(3):557-67
pubmed: 22147368
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
PeerJ. 2014 Sep 30;2:e603
pubmed: 25289188
Brief Bioinform. 2012 Nov;13(6):669-81
pubmed: 22962338
Genome Biol. 2015 Dec 09;16:276
pubmed: 26653756
Bioinformatics. 2016 Apr 1;32(7):1088-90
pubmed: 26614127
Nat Biotechnol. 2013 Jun;31(6):533-8
pubmed: 23707974
BMC Genomics. 2018 May 8;19(1):332
pubmed: 29739332
PeerJ. 2015 Oct 08;3:e1319
pubmed: 26500826
Nat Biotechnol. 2017 Aug 8;35(8):725-731
pubmed: 28787424
Science. 2013 Nov 29;342(6162):1057-8
pubmed: 24288324
Environ Microbiol. 2013 Jun;15(6):1882-99
pubmed: 23387867