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A probabilistic model to recover individual genomes from metagenomes

Johannes Dröge, Alexander Schönhuth, Alice C. McHardy
2017 PeerJ Computer Science  
We present a versatile probabilistic model for genome recovery and analysis, which aggregates three types of information that are commonly used for genome recovery from metagenomes.  ...  Recovering their genomes is a crucial but very challenging step due to the complexity of the underlying biological system and technical factors.  ...  Reimering, A. Weimann, and A. Bremges for proofreading and constructive feedback. ADDITIONAL INFORMATION AND DECLARATIONS Funding The authors received no funding for this work.  ... 
doi:10.7717/peerj-cs.117 fatcat:f5g7g6tudnftrdk5zd4s5d5hyu

A robust statistical framework for reconstructing genomes from metagenomic data [article]

Dongwan Don Kang, Jeff Froula, Rob Egan, Zhong Wang
2014 bioRxiv   pre-print
We present software that reconstructs genomes from shotgun metagenomic sequences using a reference-independent approach.  ...  Applying MetaBAT to a human gut microbiome dataset identified 173 highly specific genomes bins including many representing previously unidentified species.  ...  Detecting individual draft genomes in a process called metagenome binning (1,2) provides a substitute for direct isolation.  ... 
doi:10.1101/011460 fatcat:f5wivsod5jcvtfkweuqcp6qwny

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

Dongwan D. Kang, Jeff Froula, Rob Egan, Zhong Wang
2015 PeerJ  
Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions  ...  Here we introduce automated software called MetaBAT that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency for accurate metagenome binning.  ...  The work was conducted by the US Department of Energy Joint Genome Institute.  ... 
doi:10.7717/peerj.1165 pmid:26336640 pmcid:PMC4556158 fatcat:odsbsphyvnhbxbjmjhesvjsgyi

Computational Methods For Taxonomic Annotation And Genome Reconstruction In Metagenomics

Johannes Dröge, Alice C. McHardy
2017 Zenodo  
Metagenomics is a field dedicated to the genetic analysis of such communities.  ...  Apart from its considerable economic potential, metagenomic approaches lead to a fundamentally improved understanding of the microbial processes on earth.  ...  Genome bin refinement We applied the model to show one of its current use cases on more realistic data. We downloaded the medium complexity dataset from www.cami-challenge.org.  ... 
doi:10.5281/zenodo.1263098 fatcat:eribyymx3zatpbsrxphmc3ugje

Recovering Individual Genomes from Metagenomes Using MaxBin 2.0

Yu-Wei Wu, Steven W Singer
2021 Scientia Fungorum  
We thus developed a database-free method, MaxBin 2.0, to aid in the process of recovering microbial genomes from metagenomes in a de novo manner.  ...  It is critical to identify individual genomes from microbiomic samples in order to carry out analysis of the microbes.  ...  Acknowledgment This work is supported by Taiwan Ministry of Science and Technology grant MOST108-2628-E-038-002-MY3 to Y.-W.W.  ... 
doi:10.1002/cpz1.128 pmid:33961733 fatcat:xfhghi6bijbhvcwp7dpuuktp2m

On the complexity of haplotyping a microbial community [article]

Samuel M Nicholls, Wayne Aubrey, Kurt de Grave, Leander Schietgat, Christopher J M Creevey, Amanda Clare
2020 bioRxiv   pre-print
This work describes and formalizes the problem of recovering genes (and other genomic subsequences) from all individuals within a complex community sample: which we term the metagenomic individual haplotyping  ...  A significant obstacle to this goal arises from the lack of a computationally tractable solution that can recover these sequences from sequenced read fragments.  ...  All authors contributed to the manuscript. Acknowledgements SN wishes to acknowledge Nicholas Loman (University of Birmingham) for supporting the completion of the manuscript.  ... 
doi:10.1101/2020.08.10.244848 fatcat:42zrxsmuobgw3jb5zbw42pkbla

Computational haplotype recovery and long-read validation identifies novel isoforms of industrially relevant enzymes from natural microbial communities [article]

Samuel M Nicholls, Wayne Aubrey, Arwyn Edwards, Kurt de Grave, Sharon Huws, Leander Schietgat, André Soares, Christopher J Creevey, Amanda Clare
2017 bioRxiv   pre-print
") of the genes and genomes of every individual present.  ...  To overcome this, we present Hansel and Gretel: a novel probabilistic framework that reconstructs the most likely haplotypes from complex microbiomes, is robust to sequencing error and uses all available  ...  haplotypes from a metagenome.  ... 
doi:10.1101/223404 fatcat:agvsuwt7mjblbaclojsjru2jru

Recovering complete and draft population genomes from metagenome datasets

Naseer Sangwan, Fangfang Xia, Jack A. Gilbert
2016 Microbiome  
Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success.  ...  Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture  ...  MaxBin and MetaBAT do not use straight Euclidean distance but estimate probabilistic composition distributions from complete reference genomes.  ... 
doi:10.1186/s40168-016-0154-5 pmid:26951112 pmcid:PMC4782286 fatcat:j3cdxxmq4beiddgbcinmafh5xe

Probabilistic Recovery Of Cryptic Haplotypes From Metagenomic Data [article]

Samuel M Nicholls, Wayne Aubrey, Kurt de Grave, Leander Schietgat, Christopher J Creevey, Amanda Clare
2017 bioRxiv   pre-print
for any particular genomic region of interest within a metagenomic dataset.  ...  To address this, we have developed a novel probabilistic approach for reconstructing haplotypes from complex microbial communities and propose the "metahaplome" as a definition for the set of haplotypes  ...  Disclosure Declaration The authors have no conflict of interest to declare.  ... 
doi:10.1101/117838 fatcat:m2jleddcnrgwxpzikcdw4xgaxq

Advances in the recovery of haplotypes from the metagenome [article]

Samuel M Nicholls, Wayne Aubrey, Kurt de Grave, Leander Schietgat, Chris J Creevey, Amanda Clare
2016 bioRxiv   pre-print
Recovery, or assembly of haplotypes has proved computationally difficult and there exist many probabilistic heuristics that attempt to recover the original haplotypes for a single organism of known ploidy  ...  We evaluate our approach using synthetic metahaplomes constructed from sets of real genes and show that up to 99% of SNPs on a haplotype can be correctly recovered from short reads that originate from  ...  Acknowledgments Disclosure Declaration The authors have no conflict of interest to declare.  ... 
doi:10.1101/067215 fatcat:7exfhksubna35anns6nnphizme

Sequencing and Analysis of Neanderthal Genomic DNA

J. P. Noonan, G. Coop, S. Kudaravalli, D. Smith, J. Krause, J. Alessi, F. Chen, D. Platt, S. Paabo, J. K. Pritchard, E. M. Rubin
2006 Science  
To this end, we developed a direct genomic selection approach to recover known and unknown sequences from metagenomic ancient DNA libraries (Fig. 7) (24) .  ...  We first attempted to recover specific sequences from a Pleistocene cave bear metagenomic library we previously constructed.  ... 
doi:10.1126/science.1131412 pmid:17110569 pmcid:PMC2583069 fatcat:5tw4xwtlu5byrnabel47o6tqhi

DIME: A Novel Framework for De Novo Metagenomic Sequence Assembly

Xuan Guo, Ning Yu, Xiaojun Ding, Jianxin Wang, Yi Pan
2015 Journal of Computational Biology  
and three real metagenomic sequence datasets with various reads from fifty thousand to a couple million in size.  ...  To address this limitation and promote both accuracy and efficiency, we develop a novel metagenomic sequence assembly framework, DIME, by taking the DIvide, conquer, and MErge strategies.  ...  How to remove the chimeric reads (Lasken & Stockwell, 2007) , that is, a prefix or a suffix matching distant locations in the genome. 2.4.1. Generative probabilistic model.  ... 
doi:10.1089/cmb.2014.0251 pmid:25684202 pmcid:PMC4326031 fatcat:k6ahscslcvacziyp6qeqqip3qq

On the complexity of haplotyping a microbial community

Samuel M Nicholls, Wayne Aubrey, Kurt De Grave, Leander Schietgat, Christopher J Creevey, Amanda Clare, Pier Luigi Martelli
2020 Bioinformatics  
This work describes and formalizes the problem of recovering genes (and other genomic subsequences) from all individuals within a complex community sample, which we term the metagenomic individual haplotyping  ...  A significant obstacle to this goal arises from the lack of a computationally tractable solution that can recover these sequences from sequenced read fragments.  ...  Acknowledgements S.N. wishes to acknowledge Nicholas Loman (University of Birmingham) for supporting the completion of the manuscript.  ... 
doi:10.1093/bioinformatics/btaa977 pmid:33444437 pmcid:PMC8208737 fatcat:qpc63gf7tfewxgekz4wdpf6oni

To Petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics

R A Leo Elworth, Qi Wang, Pavan K Kota, C J Barberan, Benjamin Coleman, Advait Balaji, Gaurav Gupta, Richard G Baraniuk, Anshumali Shrivastava, Todd J Treangen
2020 Nucleic Acids Research  
In recent years, the accelerated pace of genomic data availability has been accompanied by the application of a wide array of highly efficient approaches from other fields to the field of metagenomics.  ...  As computational biologists continue to be inundated by ever increasing amounts of metagenomic data, the need for data analysis approaches that keep up with the pace of sequence archives has remained a  ...  However, method development to date has been primarily focused on genome sequencing for a single individual or isolate genome.  ... 
doi:10.1093/nar/gkaa265 pmid:32338745 fatcat:v4julw322nc47kgb7q7urkkkci

Epidemiological, clinical and zoonotic evidences for the existence of Lyme disease in Central of Mexico

G. Gordillo, F. Solorzano Santos, J. Torres, E. Velazquez, G. Ramon, R. Garcia, M. Vargas
2010 International Journal of Infectious Diseases  
Several closely related virus genomes were recovered from individual samples; however, viruses from different samples varied widely, indicating distinct virus profiles.  ...  As mosquitoes draw blood from animals and humans and are known to carry a number of viruses, metagenomic sequencing of viral particles purified from mosquitoes enables surveillance of the animal viruses  ...  Several closely related virus genomes were recovered from individual samples; however, viruses from different samples varied widely, indicating distinct virus profiles.  ... 
doi:10.1016/j.ijid.2010.02.462 fatcat:n2kerq3ujzborcuzadiqvps5ya
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