A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2013; you can also visit the original URL.
The file type is application/pdf.
Filters
ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies
2013
Computer applications in the biosciences : CABIOS
Preserved Fulltext
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
2013
2013 IEEE International Conference on Bioinformatics and Biomedicine
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2015
Journal of Computational Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2018
FEMS Microbiology Ecology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2021
PeerJ
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2010
BMC Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2014
BMC Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2013
Computer applications in the biosciences : CABIOS
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2013
BMC Research Notes
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2017
Zenodo
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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]
2017
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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]
2014
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2014
Frontiers in Plant Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2016
Applied and Translational Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2014
BMC Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 848 results