CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Genome Research

Volumn 25, Issue 7, 2015, Pages 1043-1055

  Parks, Donovan H ^a   Imelfort, Michael ^a   Skennerton, Connor T ^a   Hugenholtz, Philip ^a   Tyson, Gene W ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CAPNOCYTOPHAGA; CLOSTRIDIALES; GENE AMPLIFICATION; GENE LOCATION; GENE LOSS; GENOME ANALYSIS; GENOME SIZE; GENOMIC FRAGMENT; GENOMICS; LACTOBACILLUS GASSERI; MARKER GENE; METAGENOME; METAGENOMICS; MICROBIAL GENOME; NONHUMAN; OPERON; PARACOCCUS DENITRIFICANS; PHYLOGENY; PRIORITY JOURNAL; SIMULATION; TAXONOMY; PROCEDURES;

ARCHAEA; BACTERIA (MICROORGANISMS);

GENOME, MICROBIAL; METAGENOME; METAGENOMICS;

EID: 84937040910     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.186072.114     Document Type: Article

References (47)

1. Akhter S, Aziz RK, Edwards RA. 2012. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res 40: e126.
2. Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. 2013. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 31: 533-538.
3. Brady A, Salzberg SL. 2009. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods 6: 673-676.
4. Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, et al. 2009. Genome project standard in a new era of sequencing. Science 326: 236-237.
5. Darling AE, Jospin G, Lowe E, Matsen FA IV, Bik HM, Eisen JA. 2014. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2: e243.
6. Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC, Yelton AP, Banfield JF. 2010. Community-wide analysis of microbial genome sequences signatures. Genome Biol 10: R85.
7. Dröge J, Gregor I, McHardy AC. 2014. Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods. Bioinformatics 31: 817-824.
8. Dupont CL, Rusch DB, Yooseph S, Lombardo MJ, Richter RA, Valas R, Novotny M, Yee-Greenbaum J, Selengut JD, Haft DH, et al. 2012. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J 6: 1186-1199.
9. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. 2008. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 26: 541-547.
10. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, et al. 2014. Pfam: the protein families database. Nucleic Acids Res 42: D222-D230.
11. Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 15: 1072-1075.
12. Haft DH, Selengut JD, White O. 2003. The TIGRFAMs database of protein families. Nucleic Acids Res 31: 371-373.
13. Haroon MF, Hu S, Shi Y, Imelfort M, Keller J, Hugenholtz P, Yuan Z, Tyson GW. 2013. Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature 500: 567-570.
14. Hyatt D, Locascio PF, Hauser LJ, Uberbacher EC. 2012. Gene and translation initiation site prediction in metagenomic sequences. Bioinformatics 28: 2223-2230.
15. Imelfort M, Parks DH, Woodcroft BJ, Dennis P, Hugenholtz P, Tyson GW. 2014. GroopM: an automated tool for the recovery of population genomes from related metagenomes. PeerJ 2: e603.
16. Jørgensen TS, Xu Z, Hansen MA, Sørensen SJ, Hansen LH. 2014. Hundreds of circular novel plasmids and DNA elements identified in a rat cecum metamobilome. PLoS One 9: e87924.
17. Konstantinidis KT, Tiedje JM. 2005. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187: 6258-6264.
18. Langille MGI, Hsiao WWL, Brinkman FSL. 2010. Detecting genomic islands using bioinformatics approaches. Nat Rev Microbiol 8: 373-382.
19. Mardis E, McPherson J, Martienssen R, Wilson RK, McCombie WR. 2002. What is finished, and why does it matter. Genome Res 12: 669-671.
20. Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Pillay M, Ratner A, Huang J, Woyke T, Huntemann M, et al. 2014. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res 42: D560-D567.
21. Matsen FA, Kodner RB, Armbrust EV. 2010. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 11: 538.
22. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P. 2012. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6: 610-618.
23. Mende DR, Sunagawa S, Zeller G, Bork P. 2013. Accurate and universal delineation of prokaryotic species. Nat Methods 10: 881-884.
24. Meyerdierks A, Kube M, Kostadinov I, Teeling H, Glöckner FO, Reinhardt R, Amann R. 2010. Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group. Environ Microbiol 12: 422-439.
25. Parks DH, MacDonald N, Beiko R. 2011. Classifying short genomic fragments from novel lineages using composition and homology. BMC Bioinformatics 12: 328.
26. Patil KR, Haider P, Pope PB, Turnbaugh PJ, Morrison M, Scheffer T, McHardy AC. 2011. Taxonomic metagenome sequence assignment with structured output models. Nat Methods 8: 191-192.
27. Price MN, Dehal PS, Arkin AP. 2009. FastTree: computing large minimum-evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26: 1641-1650.
28. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, et al. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499: 431-437.
29. Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, et al. 2012. GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res 22: 557-567.
30. Segata N, Börnigen D, Morgan XC, Huttenhower C. 2013. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 4: 2304.
31. Sekiguchi Y, Ohashi A, Parks DH, Yamauchi T, Tyson GW, Hugenholtz P. 2015. First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking. PeerJ 3: e740.
32. Sharon I, Banfield JF. 2013. Genome from metagenomics. Science 342: 1057-1058.
33. Sharon I, Morowitz MJ, Thomas BC, Costello EK, Relman DA, Banfield JF. 2013. Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res 23: 111-120.
34. Shih PM, Wu D, Latifi A, Axen SD, Fewer DP, Talla E, Calteau A, Cai F, Tandeau de Marsac N, Rippka R, et al. 2013. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc Natl Acad Sci 110: 1053-1058.
35. Siddavattam D, Karegoudar TN, Modde SK, Kumar N, Baddam R, Avasthi TS, Ahmed N. 2011. Genome of a novel isolate of Paracoccus denitrificans capable of degrading N,N-dimethylformamide. J Bacteriol 193: 5598-5599.
36. Soo RM, Skennerton CT, Sekiguchi Y, Imelfort M, Paech SJ, Dennis PG, Steen JA, Parks DH, Tyson GW, Hugenholtz P. 2014. An expanded genomic representation of the phylum Cyanobacteria. Genome Biol Evol 6: 1031-1045.
37. Sukumaran J, Holder MT. 2010. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26: 1569-1571.
38. Swan BK, Tupper B, Sczyrba A, Lauro FM, Martinez-Garcia M, González JM, Luo H, Wright JJ, Landry ZC, Hanson NW, et al. 2013. Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proc Natl Acad Sci 110: 11463-11468.
39. Turnbaugh PJ, Ley RE, Hamady M, Frader-Liggett CM, Knight R, Gordon JI. 2007. The human microbiome project. Nature 449: 804-810.
40. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43.
41. Whelan S, Goldman N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18: 691-699.
42. Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, Wilkins MJ, Hettich RL, Lipton MS, Williams KH, et al. 2012. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science 337: 1661-1665.
43. Wu M, Scott AJ. 2012. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 28: 1033-1034.
44. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. 2009. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462: 1056-1060.
45. Wu D, Doroud L, Eisen JA. 2013. TreeOTU: operational taxonomic unit classification based on phylogenetic trees. arXiv 1308.6333v1.
46. Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol 39: 306-314.
47. Yutin N, Galperin MY. 2013. A genomic update on clostridial phylogeny: gram-negative spore formers and other misplaced clostridia. Environ Microbiol 15: 2631-2641.