Motley ST, Picuri JM, Crowder CD, Minich JJ, Hofstadler SA, Eshoo MW. Improved multiple displacement amplification (imda) and ultraclean reagents. BMC Genom. 2014;15:443.Article
Google Scholar
Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014;12(87):87.Article
PubMed
PubMed Central
Google Scholar
Riesenfeld CS, Schloss PD, Handelsman J, et al. Metagenomics: genomic analysis of microbial communities. Annu Rev Genet. 2004;38(1):525–52.Article
CAS
PubMed
Google Scholar
Alberts B. Molecular biology of the cell. Garland Science. NewYork: Taylor and Francis Group; 2015.
Google Scholar
Wooley JC, Godzik A, Friedberg I. A primer on metagenomics. PLoS Comput Biol. 2010;6(2):1–13.Article
Google Scholar
Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol. 2013;31(6):533–8.Article
CAS
PubMed
Google Scholar
Sangwan N, Xia F, Gilbert JA. Recovering complete and draft population genomes from metagenome datasets. Microbiome. 2016;4:1–11. https://doi.org/10.1186/s40168-016-0154-5.Article
Google Scholar
Sedlar K, Kupkova K, Provaznik I. Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics. Comput Struct Biotechnol J. 2017;15:48–55. https://doi.org/10.1016/j.csbj.2016.11.005.Article
CAS
PubMed
Google Scholar
Mallawaarachchi V, Wickramarachchi A, Lin Y. Graphbin: refined binning of metagenomic contigs using assembly graphs. Bioinformatics. 2020;36:3307–13. https://doi.org/10.1093/bioinformatics/btaa180.Article
CAS
PubMed
Google Scholar
MacKelprang R, Waldrop MP, Deangelis KM, David MM, Chavarria KL, Blazewicz SJ, Rubin EM, Jansson JK. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature. 2011;480:368–71. https://doi.org/10.1038/nature10576.Article
CAS
PubMed
Google Scholar
Ghai R, Mizuno CM, Picazo A, Camacho A, Rodriguez-Valera F. Key roles for freshwater actinobacteria revealed by deep metagenomic sequencing. Mol Ecol. 2014;23:6073–90. https://doi.org/10.1111/mec.12985.Article
CAS
PubMed
Google Scholar
Hua ZS, Han YJ, Chen LX, Liu J, Hu M, Li SJ, Kuang JL, Chain PS, Huang LN, Shu WS. Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics. ISME J. 2015;9:1280–94. https://doi.org/10.1038/ismej.2014.212.Article
CAS
PubMed
Google Scholar
Iverson V, Morris RM, Frazar CD, Berthiaume CT, Morales RL, Armbrust EV. Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science. 2012;335:587–90. https://doi.org/10.1126/science.1212665.Article
CAS
PubMed
Google Scholar
Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC, Yelton AP, Banfield JF. Community-wide analysis of microbial genome sequence signatures. Genome Biol. 2009;10:1–16. https://doi.org/10.1186/gb-2009-10-8-r85.Article
CAS
Google Scholar
Lander ES, Waterman MS. Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics. 1988;2:231–9. https://doi.org/10.1016/0888-7543(88)90007-9.Article
CAS
PubMed
Google Scholar
Wu YW, Ye Y. A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. J Comput Biol. 2011;18:523–34. https://doi.org/10.1089/cmb.2010.0245.Article
CAS
PubMed
PubMed Central
Google Scholar
…Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Chatelier EL, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Santos MBQD, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Leonard P, Levenez F, Lund O, Moumen B, Paslier DL, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD, Jamet A, Mérieux A, Cultrone A, Torrejon A, Quinquis B, Brechot C, Delorme C, M’rini C, Vos WM, Maguin E, Varela E, Guedon E, Gwen F, Haimet F, Artiguenave F, Vandemeulebrouck G, Denariaz G, Khaci G, Knol H, Knol J, Weissenbach J, Hylckama Vlieg JET, Torben J, Parkhill J, Turner K, Guchte M, Antolin M, Rescigno M, Kleerebezem M, Derrien M, Galleron N, Sanchez N, Grarup N, Veiga P, Oozeer R, Dervyn R, Layec S, Bruls T, Winogradski Y, Erwin Z. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol. 2014;32:822–8. https://doi.org/10.1038/nbt.2939.Article
CAS
PubMed
Google Scholar
Lin HH, Liao YC. Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes. Sci Rep. 2016;6:24175. https://doi.org/10.1038/srep24175.Article
CAS
PubMed
PubMed Central
Google Scholar
Alneberg J, Bjarnason BS, Bruijn I, Schirmer M, Quick J, Ijaz UZ, Lahti L, Loman NJ, Andersson AF, Quince C. Binning metagenomic contigs by coverage and composition. Nat Methods. 2014;11(11):1144–6. https://doi.org/10.1038/nmeth.3103.Article
CAS
PubMed
Google Scholar
Qian J, Comin M. MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage. BMC Bioinf. 2019;20:9. https://doi.org/10.1186/s12859-019-2904-4.Article
Google Scholar
Wu YW, Simmons BA, Singer SW. Maxbin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2016;32:605–7. https://doi.org/10.1093/bioinformatics/btv638.Article
CAS
PubMed
Google Scholar
Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, Wang Z. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019;7:7359. https://doi.org/10.7717/peerj.7359.Article
Google Scholar
Wang Z, Wang Z, Lu YY, Sun F, Zhu S. Solidbin: improving metagenome binning with semi-supervised normalized cut. Bioinformatics. 2019;35(21):4229–38.Article
CAS
PubMed
PubMed Central
Google Scholar
Laczny CC, Kiefer C, Galata V, Fehlmann T, Backes C, Keller A. Busybee web: metagenomic data analysis by bootstrapped supervised binning and annotation. Nucleic Acids Res. 2017;45(W1):171–9.Article
Google Scholar
Wang Ziye, Huang Pingqin, You Ronghui, Sun Fengzhu, Zhu Shanfeng. metabinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities. Genome Biol. 2023;24(1):1.Article
PubMed
PubMed Central
Google Scholar
Uritskiy Gherman V, DiRuggiero Jocelyne, Taylor James. Metawrap-a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome. 2018;6(1):1–13.Article
Google Scholar
Babaiha Negin Sadat, Aghdam Rosa, Ghiam Shokoofeh, Eslahchi Changiz. nn-rnaloc: neural network-based model for prediction of mrna sub-cellular localization using distance-based sub-sequence profiles. PLoS ONE. 2023;18(9):0258793.Article
Google Scholar
Kang DD, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. Peer J. 2015;3:1165. https://doi.org/10.7717/peerj.1165.Article
CAS
Google Scholar
Lu YY, Chen T, Fuhrman JA, Sun F, Sahinalp C. Cocacola: binning metagenomic contigs using sequence composition, read coverage, co-alignment and paired-end read linkage. Bioinformatics. 2017;33:791–8. https://doi.org/10.1093/bioinformatics/btw290.Article
CAS
PubMed
Google Scholar
Likas A, Vlassis N, Verbeek JJ. The global k-means clustering algorithm. Pattern Recogn. 2003;36(2):451–61.Article
Google Scholar
Etter Paul D, Preston Jessica L, Susan Bassham, Cresko William A, Johnson Eric A. local de novo assembly of rad paired-end contigs using short sequencing reads. PLoS ONE. 2011;6(4):18561.Article
Google Scholar
Ke Zhang, Rongnan Lin, Yujun Chang, Qing Zhou, Zhi Zhang. 16s-fasas: an integrated pipeline for synthetic full-length 16s rrna gene sequencing data analysis. Peer J. 2022;10:14043.Article
Google Scholar
Sharon I, Morowitz MJ, Thomas BC, Costello EK, Relman DA, Banfield JF. Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res. 2013;23:111–20. https://doi.org/10.1101/gr.142315.112.Article
CAS
PubMed
PubMed Central
Google Scholar
…Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, Demaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiutė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Kang DD, 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, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC. Critical assessment of metagenome interpretation—a benchmark of metagenomics software. Nat Methods. 2017;14:1063–71. https://doi.org/10.1038/nmeth.4458.Article
CAS
PubMed
PubMed Central
Google Scholar
…Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, Creasy HH, Earl AM, Fitzgerald MG, Fulton RS, Giglio MG, 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 V, Brooks JP, Buck GA, Buhay CJ, Busam DA, Campbell JL, Canon SR, Cantarel BL, Chain PSG, Chen IMA, 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 WM, Durkin AS, Edgar RC, Erlich RL, Farmer CN, Farrell RM, Faust K, Feldgarden M, Felix VM, Fisher S, Fodor AA, Forney LJ, Foster L, Francesco VD, 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, Haake SK, 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, King NB, Knights D, Kong HH, Koren O, Koren S, Kota KC, Kovar CL, Kyrpides NC, Rosa PSL, 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 RD, Madden T, Mahurkar AA, Mannon PJ, Mardis ER, Markowitz VM, Mavromatis K, McCorrison JM, McDonald D, McEwen J, McGuire AL, McInnes P, Mehta T, Mihindukulasuriya KA, Miller JR, Minx PJ, Newsham I, Nusbaum C, Oglaughlin M, Orvis J, Pagani I, Palaniappan K, Patel SM, Pearson M, Peterson J, Podar M, Pohl C, Pollard KS, Pop M, 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 JF, 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 Y, 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, Methé BA, Nelson KE, Petrosino JF, Weinstock GM, Wilson RK, White O. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207–14. https://doi.org/10.1038/nature11234.Article
CAS
Google Scholar
VanVinh L, Lang TV, Binh LT, Hoai TV. A two-phase binning algorithm using l-mer frequency on groups of non-overlapping reads. Algorith Mol Biol. 2015;10:1–12. https://doi.org/10.1186/s13015-014-0030-4.Article
CAS
Google Scholar
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. Checkm: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25(7):1043–55.Article
CAS
PubMed
PubMed Central
Google Scholar
der Maaten Van, Laurens Hinton Geoffrey. Visualizing data using t-SNE. J Mach Learn Res. 2008;9(11):2579–605.
Google Scholar
Xu X, Xie Z, Yang Z, Li D, Xu X. A t-SNE based classification approach to compositional microbiome data. Front Genet. 2020;11: 620143.Article
PubMed
PubMed Central
Google Scholar
Zhou Fengfeng, Olman Victor, Xu Ying. Barcodes for genomes and applications. BMC Bioinf. 2008;9(1):1–11.Article
Google Scholar