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ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies

Scott C. Clark, Rob Egan, Peter I. Frazier, Zhong Wang
2013 Computer applications in the biosciences : CABIOS  
Motivation: Researchers need general purpose methods for objectively evaluating the accuracy of single and metagenome assemblies and for automatically detecting any errors they may contain.  ...  Results: In this article, we present an Assembly Likelihood Evaluation (ALE) framework that overcomes these limitations, systematically evaluating the accuracy of an assembly in a reference-independent  ...  The authors would also like to thank the JGI Genome Technology Group for the use of their sequence data and expertise and Matthew Blow, Alex Copeland and Aleah Caulin for helpful edits and suggestions.  ... 
doi:10.1093/bioinformatics/bts723 pmid:23303509 fatcat:dwn3xlcl5raixa7gd6ak7a7mdy

De novo likelihood-based measures for comparing metagenomic assemblies

Christopher M. Hill, Irina Astrovskaya, Howard Huang, Sergey Koren, Atif Memon, Todd J. Treangen, Mihai Pop
2013 2013 IEEE International Conference on Bioinformatics and Biomedicine  
Assessing and comparing the quality of single genome assembly still relies on the availability of independently determined standards, such as manually curated genomic sequences.  ...  Thus, we must rely on de novo methods for assessing and comparing assembly qualities.  ...  ACKNOWLEDGMENT The authors would like to thank the members of the Pop lab for valuable discussions on all aspects of our work. This work was supported in part by the NIH, grant R01-  ... 
doi:10.1109/bibm.2013.6732469 dblp:conf/bibm/HillAHKMTP13 fatcat:yueh6vu5nbcgpbro3xogyh5c7q

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  
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.  ...  The recently developed next generation sequencing platforms not only decrease the cost for metagenomics data analysis, but also greatly enlarge the size of metagenomic sequence datasets.  ...  This work is also supported in part by the National Natural Science Foundation of China under grant numbers 61379108 and 61232001.  ... 
doi:10.1089/cmb.2014.0251 pmid:25684202 pmcid:PMC4326031 fatcat:k6ahscslcvacziyp6qeqqip3qq

MetaCompare: a computational pipeline for prioritizing environmental resistome risk

Min Oh, Amy Pruden, Chaoqi Chen, Lenwood S Heath, Kang Xia, Liqing Zhang
2018 FEMS Microbiology Ecology  
Based on the assembled metagenomes, samples are projected into a 3-dimensionalhazard space and assigned resistome risk scores.  ...  While numerous studies have highlighted the importance of environmental sources and pathways of the spread of antibiotic resistance, a systematic means of comparing and prioritizing risks represented by  ...  Human health risk assessment provides a quantitative framework for estimating the likelihood of illness given a specific exposure route and dose (U.S. Environmental Protection Agency (U.S.  ... 
doi:10.1093/femsec/fiy079 pmid:29718191 pmcid:PMC5995210 fatcat:6zll2wzbfzhmncy6snqubjrtlu

PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly

Maxime Borry, Alexander Hübner, Adam B. Rohrlach, Christina Warinner
2021 PeerJ  
To address these challenges, we designed PyDamage, a robust, automated approach for aDNA damage estimation and authentication of de novo assembled aDNA.  ...  DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads.  ...  ACKNOWLEDGEMENTS We thank Nigel Bean and Jonathon Tuke for extremely useful discussions. ADDITIONAL INFORMATION AND DECLARATIONS  ... 
doi:10.7717/peerj.11845 fatcat:mrlsgow4onhz3fv4z6s32yxhmq

MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

Manuel Stark, Simon A Berger, Alexandros Stamatakis, Christian von Mering
2010 BMC Genomics  
Likelihood to assign these with the best possible accuracy.  ...  However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing problem.  ...  Acknowledgements This work was supported by the Swiss National Science Foundation, by the University of Zurich through its Research Priority Program "Systems Biology and Functional Genomics", and by the  ... 
doi:10.1186/1471-2164-11-461 pmid:20687950 pmcid:PMC3091657 fatcat:kp6ddwfd4fb5jag4hej4bnbr2i

Transcriptome assembly and quantification from Ion Torrent RNA-Seq data

Serghei Mangul, Adrian Caciula, Sahar Al Seesi, Dumitru Brinza, Ion Mӑndoiu, Alex Zelikovsky
2014 BMC Genomics  
Our approach explores transcriptome structure and incorporates a maximum likelihood model into the assembly and quantification procedure.  ...  Experimental results suggest increased transcriptome assembly and quantification accuracy of MaLTA-IsoEM solution compared to existing state-of-the-art approaches.  ...  generated from a single genomic locus.  ... 
doi:10.1186/1471-2164-15-s5-s7 pmid:25082147 pmcid:PMC4120146 fatcat:2pqjoiiqafgylft7tskibudnjy

Analyzing genome coverage profiles with applications to quality control in metagenomics

Martin S. Lindner, Maximilian Kollock, Franziska Zickmann, Bernhard Y. Renard
2013 Computer applications in the biosciences : CABIOS  
The framework is evaluated on simulated data as well as applied to a large-scale metagenomic study, for which we compute the validity of 75 microbial genomes.  ...  We introduce use cases with focus on metagenomics and develop new analysis strategies to assess the validity of a reference genome with respect to (meta-) genomic read data.  ...  ACKNOWLEDGEMENTS We would like to thank Junjie Qin (BGI-Shenzhen) for help with metagenomic reference genomes and Martina Fischer and Robert Rentzsch (NG4, Robert Koch-Institut) for critical reading of  ... 
doi:10.1093/bioinformatics/btt147 pmid:23589648 fatcat:hqnlp7r3bvgpxozkycykpad5ma

De novo likelihood-based measures for comparing genome assemblies

Mohammadreza Ghodsi, Christopher M Hill, Irina Astrovskaya, Henry Lin, Dan D Sommer, Sergey Koren, Mihai Pop
2013 BMC Research Notes  
Despite decades of research in this field and the development of dozens of genome assemblers, assessing and comparing the quality of assembled genome sequences still relies on the availability of independently  ...  Conclusion: Likelihood-based measures, such as ours proposed here, will become the new standard for de novo assembly evaluation.  ...  other members of the Pop lab for valuable discussions on all aspects of our work.  ... 
doi:10.1186/1756-0500-6-334 pmid:23965294 pmcid:PMC3765854 fatcat:7n6ro7qikngtniov7wbns43qvy

Computational Methods For Taxonomic Annotation And Genome Reconstruction In Metagenomics

Johannes Dröge, Alice C. McHardy
2017 Zenodo  
Depending on the size and complexity of the metagenome, this task can be very difficult. This thesis describes two methods for assigning metagenomic sequences to taxonomic groups or genomes.  ...  Metagenomics is a field dedicated to the genetic analysis of such communities.  ...  We also retrieved the results of two highest-performing automatic binning programs, MaxBin and Metawatt, in the CAMI challenge evaluation (Sczyrba et al., 2017).  ... 
doi:10.5281/zenodo.1263098 fatcat:eribyymx3zatpbsrxphmc3ugje

GATTACA: Lightweight Metagenomic Binning With Compact Indexing Of Kmer Counts And MinHash-based Panel Selection [article]

Victoria Popic, Volodymyr Kuleshov, Michael Snyder, Serafim Batzoglou
2017 bioRxiv   pre-print
We introduce GATTACA, a framework for rapid and accurate binning of metagenomic contigs from a single or multiple metagenomic samples into clusters associated with individual species.  ...  the reference panel index can be computed offline and 6x faster for online co-abundance estimation.  ...  In particular, we present GATTACA, a lightweight framework for metagenomic binning, which (1) avoids read alignment without loss of accuracy and (2) enables efficient stand-alone analysis of single metagenomic  ... 
doi:10.1101/130997 fatcat:a4xzz3vf4vaghaplsqmygcs6ni

Automated ensemble assembly and validation of microbial genomes [article]

Sergey Koren, Todd J Treangen, Christopher M Hill, Mihai Pop, Adam M Phillippy
2014 bioRxiv   pre-print
The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods.  ...  Although computationally limited to small or mid-sized genomes, this approach is the most effective and reproducible means for generating high-quality assemblies and enables users to select an assembly  ...  Clark SC, Egan R, Frazier PI, Wang Z: ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies. Bioinformatics 2013, 29(4):435-443. 11.  ... 
doi:10.1101/002469 fatcat:pu3kvhxzxncnbfks6rn4pkz4mm

An introduction to the analysis of shotgun metagenomic data

Thomas J. Sharpton
2014 Frontiers in Plant Science  
But, the analysis of metagenomic sequences is complicated due to the complex structure of the data.  ...  Specifically, it documents how metagenomes can be analyzed to quantify community structure and diversity, assemble novel genomes, identify new taxa and genes, and determine which metabolic pathways are  ...  Genovo constructs a probabilistic model of assembly and outputs the set of contigs with the highest likelihood (Laserson et al., 2011) .  ... 
doi:10.3389/fpls.2014.00209 pmid:24982662 pmcid:PMC4059276 fatcat:syz36kyuq5bizjgs4onulfrs3u

Metabolic modeling with Big Data and the gut microbiome

Jaeyun Sung, Vanessa Hale, Annette C. Merkel, Pan-Jun Kim, Nicholas Chia
2016 Applied and Translational Genomics  
Furthermore, we present a framework for characterizing the ecology of the gut microbiome based on metabolic network modeling.  ...  Also, a new paradigm for metabolic model evaluation is necessary. Herein, we outline the need for multi-omics data integration, as well as the accompanying challenges.  ...  Deep metagenomic sequencing allows assembly of full microbial genomes without the need for culture (Jeraldo et al., 2015) .  ... 
doi:10.1016/j.atg.2016.02.001 pmid:27668170 pmcid:PMC5025471 fatcat:hl3q6sv64jbenit6pb2ca4duti

ILP-based maximum likelihood genome scaffolding

James Lindsay, Hamed Salooti, Ion Măndoiu, Alex Zelikovsky
2014 BMC Bioinformatics  
The results show that SILP2 compares favorably to previous methods OPERA and MIP in both scalability and accuracy for scaffolding single genomes of up to human size, and significantly outperforms them  ...  The ILP formulation for the maximum likelihood model is shown to be flexible enough to handle metagenomic samples.  ...  Declarations The authors declare that funding for publication of the article was by the research institute of the corresponding author.  ... 
doi:10.1186/1471-2105-15-s9-s9 pmid:25253180 pmcid:PMC4168704 fatcat:ioln24ljmfcwngp24udhhylcaq
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