AMBER: Assessment of Metagenome BinnERs

Meyer F, Hofmann P, Belmann P, Garrido-Oter R, Fritz A, Sczyrba A, McHardy AC (2018)
GigaScience 7(6): giy069.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Meyer, Fernando; Hofmann, Peter; Belmann, PeterUniBi; Garrido-Oter, Ruben; Fritz, Adrian; Sczyrba, AlexanderUniBi ; McHardy, Alice C
Erscheinungsjahr
2018
Zeitschriftentitel
GigaScience
Band
7
Ausgabe
6
Art.-Nr.
giy069
ISSN
2047-217x
eISSN
2047-217X
Page URI
https://pub.uni-bielefeld.de/record/2920723

Zitieren

Meyer F, Hofmann P, Belmann P, et al. AMBER: Assessment of Metagenome BinnERs. GigaScience. 2018;7(6): giy069.
Meyer, F., Hofmann, P., Belmann, P., Garrido-Oter, R., Fritz, A., Sczyrba, A., & McHardy, A. C. (2018). AMBER: Assessment of Metagenome BinnERs. GigaScience, 7(6), giy069. https://doi.org/10.1093/gigascience/giy069
Meyer, Fernando, Hofmann, Peter, Belmann, Peter, Garrido-Oter, Ruben, Fritz, Adrian, Sczyrba, Alexander, and McHardy, Alice C. 2018. “AMBER: Assessment of Metagenome BinnERs”. GigaScience 7 (6): giy069.
Meyer, F., Hofmann, P., Belmann, P., Garrido-Oter, R., Fritz, A., Sczyrba, A., and McHardy, A. C. (2018). AMBER: Assessment of Metagenome BinnERs. GigaScience 7:giy069.
Meyer, F., et al., 2018. AMBER: Assessment of Metagenome BinnERs. GigaScience, 7(6): giy069.
F. Meyer, et al., “AMBER: Assessment of Metagenome BinnERs”, GigaScience, vol. 7, 2018, : giy069.
Meyer, F., Hofmann, P., Belmann, P., Garrido-Oter, R., Fritz, A., Sczyrba, A., McHardy, A.C.: AMBER: Assessment of Metagenome BinnERs. GigaScience. 7, : giy069 (2018).
Meyer, Fernando, Hofmann, Peter, Belmann, Peter, Garrido-Oter, Ruben, Fritz, Adrian, Sczyrba, Alexander, and McHardy, Alice C. “AMBER: Assessment of Metagenome BinnERs”. GigaScience 7.6 (2018): giy069.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Creative Commons Namensnennung 4.0 International Public License (CC-BY 4.0):

Link(s) zu Volltext(en)
Access Level
OA Open Access

0 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

28 References

Daten bereitgestellt von Europe PubMed Central.

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
Benchmark data sets, software results and reference data for the first CAMI challenge
Belmann, GigaScience Database (), 2017
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW., Genome Res. 25(7), 2015
PMID: 25977477

CAMISIM, 0
CAMISIM: Simulating metagenomes and microbial communities
Fritz, bioRxiv (), 2018
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead B, Trapnell C, Pop M, Salzberg SL., Genome Biol. 10(3), 2009
PMID: 19261174
Fast and accurate short read alignment with Burrows-Wheeler transform.
Li H, Durbin R., Bioinformatics 25(14), 2009
PMID: 19451168
MetaQUAST: evaluation of metagenome assemblies.
Mikheenko A, Saveliev V, Gurevich A., Bioinformatics 32(7), 2015
PMID: 26614127
Bioboxes: standardised containers for interchangeable bioinformatics software.
Belmann P, Droge J, Bremges A, McHardy AC, Sczyrba A, Barton MD., Gigascience 4(), 2015
PMID: 26473029

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
Assessing the accuracy of prediction algorithms for classification: an overview.
Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H., Bioinformatics 16(5), 2000
PMID: 10871264
Mining multi-label data
Tsoumakas, 2010
Objective criteria for the evaluation of clustering methods
Rand, J Am Statist Assoc 66(336), 1971
Binning metagenomic contigs by coverage and composition.
Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, Lahti L, Loman NJ, Andersson AF, Quince C., Nat. Methods 11(11), 2014
PMID: 25218180
AMBER example HTML visualization of calculated metrics
AUTHOR UNKNOWN, 0

National, 1988
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.
Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, Hugenholtz P, Tyson GW., Nat Microbiol 2(11), 2017
PMID: 28894102
The binning of metagenomic contigs for microbial physiology of mixed cultures.
Strous M, Kraft B, Bisdorf R, Tegetmeyer HE., Front Microbiol 3(), 2012
PMID: 23227024
BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation
Graham, PeerJ 5(), 2016
Recovery of genomes from metagenomes via a dereplication, aggregation, and scoring strategy
Sieber, bioRxiv (), 2017

Critical, 0

AUTHOR UNKNOWN, 2018
Supporting data for “AMBER: Assessment of Metagenome BinnERs.”
Meyer, GigaScience Database (), 2018
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 29893851
PubMed | Europe PMC

Suchen in

Google Scholar