Performance of Five Metagenomic Classifiers for Virus Pathogen Detection Using Respiratory Samples from a Clinical Cohort.
bioinformatics
next-generation sequencing
pathogen detection
viral metagenomics
Journal
Pathogens (Basel, Switzerland)
ISSN: 2076-0817
Titre abrégé: Pathogens
Pays: Switzerland
ID NLM: 101596317
Informations de publication
Date de publication:
11 Mar 2022
11 Mar 2022
Historique:
received:
21
01
2022
revised:
21
02
2022
accepted:
07
03
2022
entrez:
26
3
2022
pubmed:
27
3
2022
medline:
27
3
2022
Statut:
epublish
Résumé
Viral metagenomics is increasingly applied in clinical diagnostic settings for detection of pathogenic viruses. While several benchmarking studies have been published on the use of metagenomic classifiers for abundance and diversity profiling of bacterial populations, studies on the comparative performance of the classifiers for virus pathogen detection are scarce. In this study, metagenomic data sets (
Identifiants
pubmed: 35335664
pii: pathogens11030340
doi: 10.3390/pathogens11030340
pmc: PMC8953373
pii:
doi:
Types de publication
Journal Article
Langues
eng
Références
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Cell. 2019 Aug 8;178(4):779-794
pubmed: 31398336
Genome Biol. 2014 Mar 03;15(3):R46
pubmed: 24580807
Bioinformatics. 2019 Mar 1;35(5):871-873
pubmed: 30124794
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
Nat Rev Genet. 2019 Jun;20(6):341-355
pubmed: 30918369
J Clin Virol. 2021 Jan;134:104691
pubmed: 33278791
Genome Biol. 2019 Nov 28;20(1):257
pubmed: 31779668
Annu Rev Pathol. 2019 Jan 24;14:319-338
pubmed: 30355154
Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10915-9
pubmed: 1438297
Clin Infect Dis. 2019 Jan 1;68(1):139-142
pubmed: 29893821
J Clin Virol. 2021 Aug;141:104908
pubmed: 34273858
Nat Commun. 2016 Apr 13;7:11257
pubmed: 27071849
J Clin Virol. 2021 May;138:104812
pubmed: 33819811
PLoS One. 2019 Oct 24;14(10):e0223952
pubmed: 31647831
Bioinformatics. 2007 May 15;23(10):1282-8
pubmed: 17379688
Expert Rev Mol Diagn. 2021 Nov;21(11):1139-1146
pubmed: 34607520
Nat Methods. 2017 Nov;14(11):1063-1071
pubmed: 28967888
Genes (Basel). 2019 Aug 28;10(9):
pubmed: 31466373
Genome Biol. 2019 Mar 4;20(1):51
pubmed: 30832730
J Infect. 2018 Mar;76(3):225-240
pubmed: 29305150
Nat Methods. 2007 Jun;4(6):495-500
pubmed: 17468765
N Engl J Med. 2019 Jun 13;380(24):2327-2340
pubmed: 31189036
Genome Res. 2016 Dec;26(12):1721-1729
pubmed: 27852649
J Clin Virol. 2020 Oct;131:104594
pubmed: 32866812
Clin Microbiol Infect. 2019 Oct;25(10):1277-1285
pubmed: 31059795
Genome Biol. 2018 Nov 16;19(1):198
pubmed: 30445993
Emerg Infect Dis. 2017 Oct;23(10):1964-1968
pubmed: 28930022
J Clin Virol. 2021 Oct;143:104940
pubmed: 34416523
BMC Genomics. 2015 Mar 25;16:236
pubmed: 25879410
J Clin Microbiol. 2019 Jul 26;57(8):
pubmed: 31167846
J Mol Diagn. 2020 Feb;22(2):196-207
pubmed: 31837435
J Clin Virol. 2020 Sep;130:104566
pubmed: 32823257
Genome Res. 2017 May;27(5):824-834
pubmed: 28298430
Genome Biol. 2017 Sep 21;18(1):182
pubmed: 28934964
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Nat Methods. 2015 Jan;12(1):59-60
pubmed: 25402007
Sci Rep. 2018 Sep 13;8(1):13767
pubmed: 30213965
Nat Methods. 2021 Jun;18(6):618-626
pubmed: 33986544
Sci Rep. 2018 Aug 13;8(1):12034
pubmed: 30104688
Ann Hematol. 2016 Oct;95(11):1919-21
pubmed: 27468852
Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45
pubmed: 26553804
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Front Microbiol. 2018 Apr 23;9:749
pubmed: 29740407
Nat Rev Microbiol. 2017 Mar;15(3):161-168
pubmed: 28134265