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Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey A. Gurevich, Anton Korobeynikov, Alla Lapidus, Andrey D. Prjibelski, Alexey Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Scott R. Clingenpeel (+6 others)
2013 Journal of Computational Biology  
a mini-metagenome) and further sequences all genomes from the mini-metagenome at once.  ...  However, single-cell assembly projects are challenging due to (i) the highly nonuniform read coverage and (ii) a greatly elevated number of chimeric reads and read pairs.  ...  R.S. was supported by NSF grants OCE-1148017, OCE-821374, and OCE-1019242. T.W. and S.R.C. were funded by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231.  ... 
doi:10.1089/cmb.2013.0084 pmid:24093227 pmcid:PMC3791033 fatcat:rpfk2dfxnfetdlwta63kimmafa

Single-cell metagenomics: challenges and applications

Yuan Xu, Fangqing Zhao
2018 Protein & Cell  
Especially, by simultaneously leveraging of single-cell genomics and metagenomics, researchers can greatly improve the efficiency and accuracy of obtaining whole genome information from complex microbial  ...  Here, we review recent developments and the challenges need to be addressed in single-cell metagenomics, including potential contamination, uneven sequence coverage, sequence chimera, genome assembly and  ...  On the other hand, reads from single-cell genome can provide clues for metagenome assembly.  ... 
doi:10.1007/s13238-018-0544-5 pmid:29696589 pmcid:PMC5960468 fatcat:bniuomcgibglhoql22xsdjo7o4

Evaluating Metagenome Assembly on a Simple Defined Community with Many Strain Variants [article]

Sherine Awad, Luiz Irber, C. Titus Brown
2017 bioRxiv   pre-print
We update the reference metagenome for this mock community and detect several additional genomes in the read data set.  ...  We evaluate the performance of three metagenome assemblers, IDBA, MetaSPAdes, and MEGAHIT, on short-read sequencing of a defined "mock" community containing 64 genomes (Shakya et al. (2013)).  ...  chimeric as-364 sembly, in which a single contig is formed from multiple genomes.  ... 
doi:10.1101/155358 fatcat:nd7gc6o635hqhasbaf572vpnta

Recent advances in genomic DNA sequencing of microbial species from single cells

Roger S. Lasken, Jeffrey S. McLean
2014 Nature reviews genetics  
The vast majority of microbial species remain uncultivated and, until recently, about half of all known bacterial phyla were identified only from their 16S ribosomal RNA gene sequence. With  ...  Yooseph and J. Badger. They also acknowledge assistance with the phylogenetic tree from C. Rinke and T. Woyke. This work was supported by grants to R.S.L. from the Alfred P.  ...  . from the US National Institute of General Medical Sciences (NIH 1R01GM095373).  ... 
doi:10.1038/nrg3785 pmid:25091868 pmcid:PMC4454502 fatcat:b6ekt7eetzbt3blymovz4mbg4i

DeepMAsED: Evaluating the quality of metagenomic assemblies [article]

Mateo Rojas-Carulla, Ruth E Ley, Bernhard Schoelkopf, Nicholas D Youngblut
2019 bioRxiv   pre-print
Conclusions: DeepMAsED accurately identifies misassemblies in metagenome-assembled contigs from a broad diversity of Bacteria and Archaea without the need for reference genomes or strong modelling assumptions  ...  DeepMAsED accuracy substantially exceeds the state-of-the-art when applied to large and complex metagenome assemblies.  ...  The assembly problem is more difficult for metagenomes relative to single organism genome-assemblies due to the higher levels of sequence complexity and high prevalence of highly similar genomic regions  ... 
doi:10.1101/763813 fatcat:dw62nbvblvajvm4zb6rgtz6cny

MetaSort untangles metagenome assembly by reducing microbial community complexity

Peifeng Ji, Yanming Zhang, Jinfeng Wang, Fangqing Zhao
2017 Nature Communications  
from the sorted mini-metagenome by the complementary of the original metagenome.  ...  Novel microbial communities extend far beyond the coverage of reference databases and de novo metagenome assembly from complex microbial communities remains a great challenge.  ...  The metagenomic data generated in this study have been deposited in the BioProject database of Genbank under the accession number PRJNA357324.  ... 
doi:10.1038/ncomms14306 pmid:28112173 pmcid:PMC5264255 fatcat:2t456ak2ubffzm6pmxssfjcdku

Multiple Layers of Chimerism in a Single-Stranded DNA Virus Discovered by Deep Sequencing

M. Krupovic, N. Zhi, J. Li, G. Hu, E. V. Koonin, S. Wong, S. Shevchenko, K. Zhao, N. S. Young
2015 Genome Biology and Evolution  
Recently, a new group of ssDNA viruses with chimeric genomes has been discovered through viral metagenomics.  ...  These chimeric viruses combine capsid protein genes and replicative protein genes that, respectively, appear to have been inherited from viruses with positive-strand RNA genomes, such as tombusviruses,  ...  Acknowledgment This work was supported in part by the Intramural Research Program of the National Institute of Health, National Heart, Lung, and Blood Institute, and National Library of Medicine.  ... 
doi:10.1093/gbe/evv034 pmid:25840414 pmcid:PMC4419787 fatcat:crs4s6prjngizpyur57bj3ivwa

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

J. S. McLean, M.-J. Lombardo, J. H. Badger, A. Edlund, M. Novotny, J. Yee-Greenbaum, N. Vyahhi, A. P. Hall, Y. Yang, C. L. Dupont, M. G. Ziegler, H. Chitsaz (+8 others)
2013 Proceedings of the National Academy of Sciences of the United States of America  
A recently developed single-cell assembler, SPAdes, in combination with contig binning methods, allowed the reconstruction of genomes from these mini-metagenomes.  ...  This report also introduces a mini-metagenomic approach based on the use of high-throughput single-cell genomics techniques and assembly tools that address a widely recognized issue: how to effectively  ...  We thank the anonymous reviewers for their time and guidance to help improve the manuscript. We also thank Pamela Mishra and Mathangi Thiagarajan (J.  ... 
doi:10.1073/pnas.1219809110 pmid:23754396 pmcid:PMC3696752 fatcat:ailg3enjq5gg5ml2xrztqpcjdy

Amino acid based de Bruijn graph algorithm for identifying complete coding genes from metagenomic and metatranscriptomic short reads

Jiemeng Liu, Qichao Lian, Yamao Chen, Ji Qi
2019 Nucleic Acids Research  
As the majority of microbes lack information of genome sequences, it is essential to assemble prokaryotic genomes ab initio aiming to retrieve complete coding genes from various metabolic pathways.  ...  Here we present a protein assembler (MetaPA), based on de Bruijn graph searching on oligopeptide spaces and can be applied on both metagenomic and metatranscriptomic sequencing data.  ...  DISCUSSION In this study, we described MetaPA, a method for the assembly and prediction of protein sequences from metagenomic or metatranscriptomic short reads.  ... 
doi:10.1093/nar/gkz017 pmid:30657979 pmcid:PMC6412133 fatcat:r3akzbm2jfhv7a7pjiyykeluvq

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective

H. Teeling, F. O. Glockner
2012 Briefings in Bioinformatics  
This mini review aims to address selected opportunities and challenges of modern metagenomics from a bioinformatics perspective and hopefully will serve as a useful resource for microbial ecologists and  ...  Continual progress in next-generation sequencing allows for generating increasingly large metagenomes and studying multiple metagenomes over time or space.  ...  Furthermore, metagenome assemblers need to be more fault tolerant than genome assemblers to account for strain-level genomic heterogeneity, which on the other hand elevates the risk for chimeric assemblies  ... 
doi:10.1093/bib/bbs039 pmid:22966151 pmcid:PMC3504927 fatcat:xdfujqlljfhzjdr4ljddlznzdm

Recovery of strain-resolved genomes from human microbiome through an integration framework of single-cell genomics and metagenomics

Koji Arikawa, Keigo Ide, Masato Kogawa, Tatsuya Saeki, Takuya Yoda, Taruho Endoh, Ayumi Matsuhashi, Haruko Takeyama, Masahito Hosokawa
2021 Microbiome  
Conclusions SMAGLinker enabled us to obtain strain-resolved genomes in the mock community and human microbiota samples by assigning metagenomic sequences correctly and covering both highly conserved genes  ...  Results Our sc-metagenomics integration framework, termed SMAGLinker, uses single-cell amplified genomes (SAGs) generated using microfluidic technology as binning guides and integrates them with metagenome-assembled  ...  Acknowledgements The super-computing resource was provided by the Human Genome Center (University of Tokyo).  ... 
doi:10.1186/s40168-021-01152-4 pmid:34641955 fatcat:o4iuh6s23vc3poxjypkccn2ez4

Nanopore sequencing enables high-resolution analysis of resistance determinants and mobile elements in the human gut microbiome [article]

Denis Bertrand, Jim Shaw, Manesh Narayan, Hui Qi Amanda Ng, Senthil Kumar, Chenhao Li, Mirta Dvornicic, Janja Paliska Soldo, Jia Yu Kho, Oon Tek Ng, Timothy Barkham, Barnaby Young (+4 others)
2018 bioRxiv   pre-print
Based on evaluations with defined in vitro communities and virtual gut microbiomes, we show that it is possible to assemble near complete genomes from metagenomes with as little as 9× long read coverage  ...  The analysis of information rich whole-metagenome datasets acquired from complex microbial communities is often restricted by the fragmented nature of assembly from short-read sequencing.  ...  Overall, these results indicate that OPERA-MS is a versatile approach capable of obtaining highly contiguous and accurate genome assemblies from diverse long read metagenomic datasets.  ... 
doi:10.1101/456905 fatcat:w2atyhf6mbg6pmtewrjgqh45zu

Assembly of long error-prone reads using de Bruijn graphs

Yu Lin, Jeffrey Yuan, Mikhail Kolmogorov, Max W. Shen, Mark Chaisson, Pavel A. Pevzner
2016 Proceedings of the National Academy of Sciences of the United States of America  
genome assembly.  ...  We show how to generalize de Bruijn graphs for assembling long error-prone reads and describe the ABruijn assembler, which combines the de Bruijn graph and the OLC approaches and results in accurate genome  ...  assemblies; and Alexey Gurevich for his help with QUAST and AntiSmash.  ... 
doi:10.1073/pnas.1604560113 pmid:27956617 pmcid:PMC5206522 fatcat:w7o44agzuvckndtr7dut6zjcgi

One Bacterial Cell, One Complete Genome

Tanja Woyke, Damon Tighe, Konstantinos Mavromatis, Alicia Clum, Alex Copeland, Wendy Schackwitz, Alla Lapidus, Dongying Wu, John P. McCutcheon, Bradon R. McDonald, Nancy A. Moran, James Bristow (+2 others)
2010 PLoS ONE  
To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach  ...  No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN.  ...  We also thank Janey Lee for the amplification of the metagenomic DNA and library creation, Joel Martin for input on SNP detection and Alex Sczyrba for help with Sulcia-specific primer design.  ... 
doi:10.1371/journal.pone.0010314 pmid:20428247 pmcid:PMC2859065 fatcat:rzxs3gudt5cdbfp6gwo2asoju4

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist's Perspective - Not Only Size Matters!

John Vollmers, Sandra Wiegand, Anne-Kristin Kaster, Francisco Rodriguez-Valera
2017 PLoS ONE  
In contrast to the highly anticipated "Critical Assessment of Metagenomic Interpretation" (CAMI) challenge, which uses general mock communitybased assembler comparison we here tested assemblers on real  ...  Illumina metagenome sequencing data from natural communities of varying complexity sampled from forest soil and algal biofilms.  ...  Sixing Huang (Leibniz Institute DSMZ, Brunswick, Germany) for proof reading of S1 Appendix and their useful suggestions.  ... 
doi:10.1371/journal.pone.0169662 pmid:28099457 pmcid:PMC5242441 fatcat:yqnsms2n65huvmxy7ua463ijvm
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