Assessing taxonomic metagenome profilers with OPAL
Meyer F, Bremges A, Belmann P, Janssen S, McHardy AC, Koslicki D (2019)
Genome biology 20(1): 51.
Zeitschriftenaufsatz
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Autor*in
Meyer, Fernando;
Bremges, Andreas;
Belmann, PeterUniBi;
Janssen, StefanUniBi 
;
McHardy, Alice C;
Koslicki, David
;
McHardy, Alice C;
Koslicki, DavidEinrichtung
Abstract / Bemerkung
The explosive growth in taxonomic metagenome profiling methods over the past years has created a need for systematic comparisons using relevant performance criteria. The Open-community Profiling Assessment tooL (OPAL) implements commonly used performance metrics, including those of the first challenge of the initiative for the Critical Assessment of Metagenome Interpretation (CAMI), together with convenient visualizations. In addition, we perform in-depth performance comparisons with seven profilers on datasets of CAMI and the Human Microbiome Project. OPAL is freely available at https://github.com/CAMI-challenge/OPAL .
Erscheinungsjahr
2019
Zeitschriftentitel
Genome biology
Band
20
Ausgabe
1
Art.-Nr.
51
ISSN
1474-760X
Page URI
https://pub.uni-bielefeld.de/record/2934274
Zitieren
Meyer F, Bremges A, Belmann P, Janssen S, McHardy AC, Koslicki D. Assessing taxonomic metagenome profilers with OPAL. Genome biology. 2019;20(1): 51.
Meyer, F., Bremges, A., Belmann, P., Janssen, S., McHardy, A. C., & Koslicki, D. (2019). Assessing taxonomic metagenome profilers with OPAL. Genome biology, 20(1), 51. https://doi.org/10.1186/s13059-019-1646-y
Meyer, Fernando, Bremges, Andreas, Belmann, Peter, Janssen, Stefan, McHardy, Alice C, and Koslicki, David. 2019. “Assessing taxonomic metagenome profilers with OPAL”. Genome biology 20 (1): 51.
Meyer, F., Bremges, A., Belmann, P., Janssen, S., McHardy, A. C., and Koslicki, D. (2019). Assessing taxonomic metagenome profilers with OPAL. Genome biology 20:51.
Meyer, F., et al., 2019. Assessing taxonomic metagenome profilers with OPAL. Genome biology, 20(1): 51.
F. Meyer, et al., “Assessing taxonomic metagenome profilers with OPAL”, Genome biology, vol. 20, 2019, : 51.
Meyer, F., Bremges, A., Belmann, P., Janssen, S., McHardy, A.C., Koslicki, D.: Assessing taxonomic metagenome profilers with OPAL. Genome biology. 20, : 51 (2019).
Meyer, Fernando, Bremges, Andreas, Belmann, Peter, Janssen, Stefan, McHardy, Alice C, and Koslicki, David. “Assessing taxonomic metagenome profilers with OPAL”. Genome biology 20.1 (2019): 51.
43 References
Daten bereitgestellt von Europe PubMed Central.
CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers.
Ounit R, Wanamaker S, Close TJ, Lonardi S., BMC Genomics 16(), 2015
PMID: 25879410
Ounit R, Wanamaker S, Close TJ, Lonardi S., BMC Genomics 16(), 2015
PMID: 25879410
MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation.
Koslicki D, Falush D., mSystems 1(3), 2016
PMID: 27822531
Koslicki D, Falush D., mSystems 1(3), 2016
PMID: 27822531
DUDes: a top-down taxonomic profiler for metagenomics.
Piro VC, Lindner MS, Renard BY., Bioinformatics 32(15), 2016
PMID: 27153591
Piro VC, Lindner MS, Renard BY., Bioinformatics 32(15), 2016
PMID: 27153591
AUTHOR UNKNOWN, 0
Metagenomic microbial community profiling using unique clade-specific marker genes.
Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C., Nat. Methods 9(8), 2012
PMID: 22688413
Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C., Nat. Methods 9(8), 2012
PMID: 22688413
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences.
Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M., BMC Genomics 12 Suppl 2(), 2011
PMID: 21989143
Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M., BMC Genomics 12 Suppl 2(), 2011
PMID: 21989143
Metagenomic species profiling using universal phylogenetic marker genes.
Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Dore J, Ehrlich SD, Stamatakis A, Bork P., Nat. Methods 10(12), 2013
PMID: 24141494
Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Dore J, Ehrlich SD, Stamatakis A, Bork P., Nat. Methods 10(12), 2013
PMID: 24141494
Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing.
Koslicki D, Foucart S, Rosen G., Bioinformatics 29(17), 2013
PMID: 23786768
Koslicki D, Foucart S, Rosen G., Bioinformatics 29(17), 2013
PMID: 23786768
ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.
Koslicki D, Chatterjee S, Shahrivar D, Walker AW, Francis SC, Fraser LJ, Vehkapera M, Lan Y, Corander J., PLoS ONE 10(10), 2015
PMID: 26496191
Koslicki D, Chatterjee S, Shahrivar D, Walker AW, Francis SC, Fraser LJ, Vehkapera M, Lan Y, Corander J., PLoS ONE 10(10), 2015
PMID: 26496191
SEK: sparsity exploiting k-mer-based estimation of bacterial community composition.
Chatterjee S, Koslicki D, Dong S, Innocenti N, Cheng L, Lan Y, Vehkapera M, Skoglund M, Rasmussen LK, Aurell E, Corander J., Bioinformatics 30(17), 2014
PMID: 24812337
Chatterjee S, Koslicki D, Dong S, Innocenti N, Cheng L, Lan Y, Vehkapera M, Skoglund M, Rasmussen LK, Aurell E, Corander J., Bioinformatics 30(17), 2014
PMID: 24812337
Protein signature-based estimation of metagenomic abundances including all domains of life and viruses.
Klingenberg H, Aßhauer KP, Lingner T, Meinicke P., Bioinformatics 29(8), 2013
PMID: 23418187
Klingenberg H, Aßhauer KP, Lingner T, Meinicke P., Bioinformatics 29(8), 2013
PMID: 23418187
TIPP: taxonomic identification and phylogenetic profiling.
Nguyen NP, Mirarab S, Liu B, Pop M, Warnow T., Bioinformatics 30(24), 2014
PMID: 25359891
Nguyen NP, Mirarab S, Liu B, Pop M, Warnow T., Bioinformatics 30(24), 2014
PMID: 25359891
Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.
Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Droge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jorgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvociute M, Hansen LH, Sorensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Goker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC., Nat. Methods 14(11), 2017
PMID: 28967888
Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Droge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jorgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvociute M, Hansen LH, Sorensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Goker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC., Nat. Methods 14(11), 2017
PMID: 28967888
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.
McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, Knight R, Caporaso JG., Gigascience 1(1), 2012
PMID: 23587224
McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, Knight R, Caporaso JG., Gigascience 1(1), 2012
PMID: 23587224
UniFrac: a new phylogenetic method for comparing microbial communities.
Lozupone C, Knight R., Appl. Environ. Microbiol. 71(12), 2005
PMID: 16332807
Lozupone C, Knight R., Appl. Environ. Microbiol. 71(12), 2005
PMID: 16332807
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
QUAST: quality assessment tool for genome assemblies.
Gurevich A, Saveliev V, Vyahhi N, Tesler G., Bioinformatics 29(8), 2013
PMID: 23422339
Gurevich A, Saveliev V, Vyahhi N, Tesler G., Bioinformatics 29(8), 2013
PMID: 23422339
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
Evolution and measurement of species diversity
Whittaker RH., 1972
Whittaker RH., 1972
Gut microbiome diversity and high-fibre intake are related to lower long-term weight gain.
Menni C, Jackson MA, Pallister T, Steves CJ, Spector TD, Valdes AM., Int J Obes (Lond) 41(7), 2017
PMID: 28286339
Menni C, Jackson MA, Pallister T, Steves CJ, Spector TD, Valdes AM., Int J Obes (Lond) 41(7), 2017
PMID: 28286339
Omega-3 fatty acids correlate with gut microbiome diversity and production of N-carbamylglutamate in middle aged and elderly women.
Menni C, Zierer J, Pallister T, Jackson MA, Long T, Mohney RP, Steves CJ, Spector TD, Valdes AM., Sci Rep 7(1), 2017
PMID: 28894110
Menni C, Zierer J, Pallister T, Jackson MA, Long T, Mohney RP, Steves CJ, Spector TD, Valdes AM., Sci Rep 7(1), 2017
PMID: 28894110
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.
Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL, Owens S, Gilbert JA, Wall DH, Caporaso JG., Proc. Natl. Acad. Sci. U.S.A. 109(52), 2012
PMID: 23236140
Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL, Owens S, Gilbert JA, Wall DH, Caporaso JG., Proc. Natl. Acad. Sci. U.S.A. 109(52), 2012
PMID: 23236140
Soil-borne microbiome: linking diversity to function.
Mendes LW, Tsai SM, Navarrete AA, de Hollander M, van Veen JA, Kuramae EE., Microb. Ecol. 70(1), 2015
PMID: 25586384
Mendes LW, Tsai SM, Navarrete AA, de Hollander M, van Veen JA, Kuramae EE., Microb. Ecol. 70(1), 2015
PMID: 25586384
A mathematical theory of communication
Shannon CE., 1948
Shannon CE., 1948
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
A framework for human microbiome research.
Human Microbiome Project Consortium, Methe BA, Nelson KE, Pop M, Creasy HH, Giglio MG, Huttenhower C, Gevers D, Petrosino JF, Abubucker S, Badger JH, Chinwalla AT, Earl AM, FitzGerald MG, Fulton RS, Hallsworth-Pepin K, Lobos EA, Madupu R, Magrini V, Martin JC, Mitreva M, Muzny DM, Sodergren EJ, Versalovic J, Wollam AM, Worley KC, Wortman JR, Young SK, Zeng Q, Aagaard KM, Abolude OO, Allen-Vercoe E, Alm EJ, Alvarado L, Andersen GL, Anderson S, Appelbaum E, Arachchi HM, Armitage G, Arze CA, Ayvaz T, Baker CC, Begg L, Belachew T, Bhonagiri V, Bihan M, Blaser MJ, Bloom T, Bonazzi VR, Brooks P, Buck GA, Buhay CJ, Busam DA, Campbell JL, Canon SR, Cantarel BL, Chain PS, Chen IM, Chen L, Chhibba S, Chu K, Ciulla DM, Clemente JC, Clifton SW, Conlan S, Crabtree J, Cutting MA, Davidovics NJ, Davis CC, DeSantis TZ, Deal C, Delehaunty KD, Dewhirst FE, Deych E, Ding Y, Dooling DJ, Dugan SP, Dunne W Jr, Durkin A, Edgar RC, Erlich RL, Farmer CN, Farrell RM, Faust K, Feldgarden M, Felix VM, Fisher S, Fodor AA, Forney L, Foster L, Di Francesco V, Friedman J, Friedrich DC, Fronick CC, Fulton LL, Gao H, Garcia N, Giannoukos G, Giblin C, Giovanni MY, Goldberg JM, Goll J, Gonzalez A, Griggs A, Gujja S, Haas BJ, Hamilton HA, Harris EL, Hepburn TA, Herter B, Hoffmann DE, Holder ME, Howarth C, Huang KH, Huse SM, Izard J, Jansson JK, Jiang H, Jordan C, Joshi V, Katancik JA, Keitel WA, Kelley ST, Kells C, Kinder-Haake S, King NB, Knight R, Knights D, Kong HH, Koren O, Koren S, Kota KC, Kovar CL, Kyrpides NC, La Rosa PS, Lee SL, Lemon KP, Lennon N, Lewis CM, Lewis L, Ley RE, Li K, Liolios K, Liu B, Liu Y, Lo CC, Lozupone CA, Lunsford R, Madden T, Mahurkar AA, Mannon PJ, Mardis ER, Markowitz VM, Mavrommatis K, McCorrison JM, McDonald D, McEwen J, McGuire AL, McInnes P, Mehta T, Mihindukulasuriya KA, Miller JR, Minx PJ, Newsham I, Nusbaum C, O'Laughlin M, Orvis J, Pagani I, Palaniappan K, Patel SM, Pearson M, Peterson J, Podar M, Pohl C, Pollard KS, Priest ME, Proctor LM, Qin X, Raes J, Ravel J, Reid JG, Rho M, Rhodes R, Riehle KP, Rivera MC, Rodriguez-Mueller B, Rogers YH, Ross MC, Russ C, Sanka RK, Sankar P, Sathirapongsasuti J, Schloss JA, Schloss PD, Schmidt TM, Scholz M, Schriml L, Schubert AM, Segata N, Segre JA, Shannon WD, Sharp RR, Sharpton TJ, Shenoy N, Sheth NU, Simone GA, Singh I, Smillie CS, Sobel JD, Sommer DD, Spicer P, Sutton GG, Sykes SM, Tabbaa DG, Thiagarajan M, Tomlinson CM, Torralba M, Treangen TJ, Truty RM, Vishnivetskaya TA, Walker J, Wang L, Wang Z, Ward DV, Warren W, Watson MA, Wellington C, Wetterstrand KA, White JR, Wilczek-Boney K, Wu YQ, Wylie KM, Wylie T, Yandava C, Ye L, Ye Y, Yooseph S, Youmans BP, Zhang L, Zhou Y, Zhu Y, Zoloth L, Zucker JD, Birren BW, Gibbs RA, Highlander SK, Weinstock GM, Wilson RK, White O., Nature 486(7402), 2012
PMID: 22699610
Human Microbiome Project Consortium, Methe BA, Nelson KE, Pop M, Creasy HH, Giglio MG, Huttenhower C, Gevers D, Petrosino JF, Abubucker S, Badger JH, Chinwalla AT, Earl AM, FitzGerald MG, Fulton RS, Hallsworth-Pepin K, Lobos EA, Madupu R, Magrini V, Martin JC, Mitreva M, Muzny DM, Sodergren EJ, Versalovic J, Wollam AM, Worley KC, Wortman JR, Young SK, Zeng Q, Aagaard KM, Abolude OO, Allen-Vercoe E, Alm EJ, Alvarado L, Andersen GL, Anderson S, Appelbaum E, Arachchi HM, Armitage G, Arze CA, Ayvaz T, Baker CC, Begg L, Belachew T, Bhonagiri V, Bihan M, Blaser MJ, Bloom T, Bonazzi VR, Brooks P, Buck GA, Buhay CJ, Busam DA, Campbell JL, Canon SR, Cantarel BL, Chain PS, Chen IM, Chen L, Chhibba S, Chu K, Ciulla DM, Clemente JC, Clifton SW, Conlan S, Crabtree J, Cutting MA, Davidovics NJ, Davis CC, DeSantis TZ, Deal C, Delehaunty KD, Dewhirst FE, Deych E, Ding Y, Dooling DJ, Dugan SP, Dunne W Jr, Durkin A, Edgar RC, Erlich RL, Farmer CN, Farrell RM, Faust K, Feldgarden M, Felix VM, Fisher S, Fodor AA, Forney L, Foster L, Di Francesco V, Friedman J, Friedrich DC, Fronick CC, Fulton LL, Gao H, Garcia N, Giannoukos G, Giblin C, Giovanni MY, Goldberg JM, Goll J, Gonzalez A, Griggs A, Gujja S, Haas BJ, Hamilton HA, Harris EL, Hepburn TA, Herter B, Hoffmann DE, Holder ME, Howarth C, Huang KH, Huse SM, Izard J, Jansson JK, Jiang H, Jordan C, Joshi V, Katancik JA, Keitel WA, Kelley ST, Kells C, Kinder-Haake S, King NB, Knight R, Knights D, Kong HH, Koren O, Koren S, Kota KC, Kovar CL, Kyrpides NC, La Rosa PS, Lee SL, Lemon KP, Lennon N, Lewis CM, Lewis L, Ley RE, Li K, Liolios K, Liu B, Liu Y, Lo CC, Lozupone CA, Lunsford R, Madden T, Mahurkar AA, Mannon PJ, Mardis ER, Markowitz VM, Mavrommatis K, McCorrison JM, McDonald D, McEwen J, McGuire AL, McInnes P, Mehta T, Mihindukulasuriya KA, Miller JR, Minx PJ, Newsham I, Nusbaum C, O'Laughlin M, Orvis J, Pagani I, Palaniappan K, Patel SM, Pearson M, Peterson J, Podar M, Pohl C, Pollard KS, Priest ME, Proctor LM, Qin X, Raes J, Ravel J, Reid JG, Rho M, Rhodes R, Riehle KP, Rivera MC, Rodriguez-Mueller B, Rogers YH, Ross MC, Russ C, Sanka RK, Sankar P, Sathirapongsasuti J, Schloss JA, Schloss PD, Schmidt TM, Scholz M, Schriml L, Schubert AM, Segata N, Segre JA, Shannon WD, Sharp RR, Sharpton TJ, Shenoy N, Sheth NU, Simone GA, Singh I, Smillie CS, Sobel JD, Sommer DD, Spicer P, Sutton GG, Sykes SM, Tabbaa DG, Thiagarajan M, Tomlinson CM, Torralba M, Treangen TJ, Truty RM, Vishnivetskaya TA, Walker J, Wang L, Wang Z, Ward DV, Warren W, Watson MA, Wellington C, Wetterstrand KA, White JR, Wilczek-Boney K, Wu YQ, Wylie KM, Wylie T, Yandava C, Ye L, Ye Y, Yooseph S, Youmans BP, Zhang L, Zhou Y, Zhu Y, Zoloth L, Zucker JD, Birren BW, Gibbs RA, Highlander SK, Weinstock GM, Wilson RK, White O., Nature 486(7402), 2012
PMID: 22699610
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
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