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Commet: Comparing and combining multiple metagenomic datasets

Nicolas Maillet, Guillaume Collet, Thomas Vannier, Dominique Lavenier, Pierre Peterlongo
2014 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
We introduce COMMET ("COmpare Multiple METagenomes"), a method that provides similarity overview between all datasets of large metagenomic projects.  ...  Finally, COMMET computes a clusterization of metagenomic datasets, which is visualized by dendrogram and heatmaps.  ...  ACKNOWLEDGMENT Authors warmly thank Claire Lemaitre for her precious advices and her help designing the R functions.  ... 
doi:10.1109/bibm.2014.6999135 dblp:conf/bibm/MailletCVLP14 fatcat:lxprenti2nfrzptzb72lbf5xnu

Commet: comparing and combining multiple metagenomic datasets [article]

Maillet Nicolas, Collet Guillaume, Vanier Thomas, Lavenier Dominique, Pierre Peterlongo
2015 arXiv   pre-print
We introduce Commet ("COmpare Multiple METagenomes"), a method that provides similarity overview between all datasets of large metagenomic projects.  ...  Finally, Commet computes a clusterization of metagenomic datasets, which is visualized by dendrogram and heatmaps. Availability: http://github.com/pierrepeterlongo/commet  ...  ACKNOWLEDGMENT Authors warmly thank Claire Lemaitre for her precious advices and her help designing the R functions.  ... 
arXiv:1511.08317v1 fatcat:c3opg45imfdlrpkdz6zh2gwn6i

GATB: Genome Assembly & Analysis Tool Box

Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, Pierre Peterlongo, Dominique Lavenier
2014 Computer applications in the biosciences : CABIOS  
Comparative metagenomics aims to provide high-level information based on DNA material sequenced from different environments.  ...  For instance, the Tara Oceans project involves hundreds of datasets of more than 100M reads each.  ...  [ 1 ] 1 COMMET: comparing and combining multiple metagenomic datasets. N. Maillet, G. Collet, T. Vannier, D. Lavenier, P. Peterlongo.  ... 
doi:10.1093/bioinformatics/btu406 pmid:24990603 pmcid:PMC4184257 fatcat:lruwdsxsbvf2neaixo6ugzzfk4

Mash: fast genome and metagenome distance estimation using MinHash

Brian D. Ondov, Todd J. Treangen, Páll Melsted, Adam B. Mallonee, Nicholas H. Bergman, Sergey Koren, Adam M. Phillippy
2016 Genome Biology  
Nanopore data; and the scalable clustering of hundreds of metagenomic samples by composition.  ...  Mash extends the MinHash dimensionality-reduction technique to include a pairwise mutation distance and P value significance test, enabling the efficient clustering and search of massive sequence collections  ...  Titus Brown, and an anonymous referee for their constructive reviews; and Philip Ashton, Aleksey Jironkin, and Nicholas Loman for providing early feedback on the software.  ... 
doi:10.1186/s13059-016-0997-x pmid:27323842 pmcid:PMC4915045 fatcat:y3kmmrznojaqzhbgxhxtzya6ne

Multiple comparative metagenomics using multisetk-mer counting

Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, Dominique Lavenier, Claire Lemaitre
2016 PeerJ Computer Science  
Simka scales-up today's metagenomic projects thanks to a new parallelk-mer counting strategy on multiple datasets.ResultsExperiments on public Human Microbiome Project datasets demonstrate that Simka captures  ...  On the other hand,de novomethods, that compare the whole sets of sequences, either do not scale up on ambitious metagenomic projects or do not provide precise and exhaustive results.MethodsThese limitations  ...  Authors warmly thank, Olivier Jaillon and Thomas Vannier from Genoscope (CEA -IG -LAGE) and Stéphane Robin from INRA AgroParisTech for providing their technical, biological and statistical expertise, as  ... 
doi:10.7717/peerj-cs.94 fatcat:yszaqg6arfcppcaajymxcucz7m

Multiple Comparative Metagenomics using Multiset k-mer Counting [article]

Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, Dominique Lavenier, Claire Lemaitre
2016 arXiv   pre-print
Simka scales-up today's metagenomic projects thanks to a new parallel k-mer counting strategy on multiple datasets. Results.  ...  On the other hand, de novo methods, that compare the whole sets of sequences, either do not scale up on ambitious metagenomic projects or do not provide precise and exhaustive results. Methods.  ...  Acknowledgments Authors warmly thank, Olivier Jaillon and Thomas Vannier from Genoscope (CEA -IG -LAGE) and Stéphane Robin from INRA AgroParisTech for providing their technical, biological and statistical  ... 
arXiv:1604.02412v3 fatcat:27ayhqmh3va4fjxxeps3islvcu

Mash: fast genome and metagenome distance estimation using MinHash [article]

Brian D. Ondov, Todd J. Treangen, Páll Melsted, Adam B. Mallonee, Nicholas H. Bergman, Sergey Koren, Adam M. Phillippy
2015 bioRxiv   pre-print
Oxford Nanopore data; and the scalable clustering of hundreds of metagenomic samples by composition.  ...  Mash extends the MinHash dimensionality-reduction technique to include a pairwise mutation distance and P-value significance test, enabling the efficient clustering and search of massive sequence collections  ...  ACKNOWLEDGEMENTS The authors thank Konstantin Berlin for helpful discussions; Brian Walenz and Torsten Seemann for reviewing the draft; and Philip Ashton, Aleksey Jironkin, and Nicholas Loman for providing  ... 
doi:10.1101/029827 fatcat:5dhsgzbwtncoxkw2mumvp67u74

Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets

Jai Ram Rideout, John H. Chase, Evan Bolyen, Gail Ackermann, Antonio González, Rob Knight, J. Gregory Caporaso
2016 GigaScience  
Applications using real data demonstrate the good accuracy of these tools compared to classical approaches.  ...  To facilitate data analysis and tools dissemination, we developed Galaxy tools and tool shed repositories.  ...  YLB and OC were supported by the Brittany and Pays de la Loire regions through the Biogenouest network.  ... 
doi:10.1186/s13742-016-0133-6 pmid:27296526 pmcid:PMC4906574 fatcat:h3hwvluupvfwtcvu2hlv76tuty

INC-Seq: accurate single molecule reads using nanopore sequencing

Chenhao Li, Kern Rei Chng, Esther Jia Hui Boey, Amanda Hui Qi Ng, Andreas Wilm, Niranjan Nagarajan
2016 GigaScience  
Applications using real data demonstrate the good accuracy of these tools compared to classical approaches.  ...  To facilitate data analysis and tools dissemination, we developed Galaxy tools and tool shed repositories.  ...  YLB and OC were supported by the Brittany and Pays de la Loire regions through the Biogenouest network.  ... 
doi:10.1186/s13742-016-0140-7 pmid:27485345 pmcid:PMC4970289 fatcat:zjdetpaswrdrzmq25glo6uelby

Draft genome of the leopard gecko, Eublepharis macularius

Zijun Xiong, Fang Li, Qiye Li, Long Zhou, Tony Gamble, Jiao Zheng, Ling Kui, Cai Li, Shengbin Li, Huanming Yang, Guojie Zhang
2016 GigaScience  
Applications using real data demonstrate the good accuracy of these tools compared to classical approaches.  ...  To facilitate data analysis and tools dissemination, we developed Galaxy tools and tool shed repositories.  ...  YLB and OC were supported by the Brittany and Pays de la Loire regions through the Biogenouest network.  ... 
doi:10.1186/s13742-016-0151-4 pmid:27784328 pmcid:PMC5080775 fatcat:24e2avrm6nh6zb3geqi4rzr5o4

Tools and techniques for computational reproducibility

Stephen R. Piccolo, Michael B. Frampton
2016 GigaScience  
Applications using real data demonstrate the good accuracy of these tools compared to classical approaches.  ...  To facilitate data analysis and tools dissemination, we developed Galaxy tools and tool shed repositories.  ...  YLB and OC were supported by the Brittany and Pays de la Loire regions through the Biogenouest network.  ... 
doi:10.1186/s13742-016-0135-4 pmid:27401684 pmcid:PMC4940747 fatcat:37345ilcb5cebo7o5selinor5m

Recommendations for open data science

Melissa Gymrek, Yossi Farjoun
2016 GigaScience  
Applications using real data demonstrate the good accuracy of these tools compared to classical approaches.  ...  To facilitate data analysis and tools dissemination, we developed Galaxy tools and tool shed repositories.  ...  YLB and OC were supported by the Brittany and Pays de la Loire regions through the Biogenouest network.  ... 
doi:10.1186/s13742-016-0127-4 pmid:27195107 pmcid:PMC4870738 fatcat:4f22gijfefgj7blc6mfchuxghi

Colib'read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Éric Rivals, Claire Lemaitre, Vincent Miele, Gustavo Sacomoto, Camille Marchet, Bastien Cazaux, Amal Zine El Aabidine, Leena Salmela (+4 others)
2016 GigaScience  
Applications using real data demonstrate the good accuracy of these tools compared to classical approaches.  ...  To facilitate data analysis and tools dissemination, we developed Galaxy tools and tool shed repositories.  ...  YLB and OC were supported by the Brittany and Pays de la Loire regions through the Biogenouest network.  ... 
doi:10.1186/s13742-015-0105-2 pmid:26870323 pmcid:PMC4750246 fatcat:x3ed526vxvg6bd5bsxqvopwhga

Gigwa—Genotype investigator for genome-wide analyses

Guilhem Sempéré, Florian Philippe, Alexis Dereeper, Manuel Ruiz, Gautier Sarah, Pierre Larmande
2016 GigaScience  
Applications using real data demonstrate the good accuracy of these tools compared to classical approaches.  ...  To facilitate data analysis and tools dissemination, we developed Galaxy tools and tool shed repositories.  ...  YLB and OC were supported by the Brittany and Pays de la Loire regions through the Biogenouest network.  ... 
doi:10.1186/s13742-016-0131-8 pmid:27267926 pmcid:PMC4897896 fatcat:2h4hdmtqongejnaky7et5pfafa

Recentrifuge: robust comparative analysis and contamination removal for metagenomics [article]

Jose Manuel Marti
2017 bioRxiv   pre-print
metagenomics.  ...  Metagenomic sequencing is becoming widespread in biomedical and environmental research, and the pace is increasing even more thanks to nanopore sequencing.  ...  In 2014 it is released COMMET (40), a tool that goes a step further 184 by enabling the combination of multiple metagenomic datasets.  ... 
doi:10.1101/190934 fatcat:omtayqllwrc63aok5j24urxp3y
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