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Real Time Metagenomics: Using k-mers to annotate metagenomes

Robert A. Edwards, Robert Olson, Terry Disz, Gordon D. Pusch, Veronika Vonstein, Rick Stevens, Ross Overbeek
2012 Computer applications in the biosciences : CABIOS  
Here we present a novel approach to annotate metagenomes using unique k-mer oligopeptide sequences from 7 to 12 amino acids long.  ...  We demonstrate that k-mer-based annotations are faster and approach the sensitivity and precision of blastx-based annotations without loosing accuracy.  ...  We implemented an API and Web servers to support the annotation of metagenomes using k-mers.  ... 
doi:10.1093/bioinformatics/bts599 pmid:23047562 pmcid:PMC3519453 fatcat:h5zmdmtg2vbktoabl3sj5rdw3m

PathoLive - Real time pathogen identification from metagenomic Illumina datasets [article]

Simon H. Tausch, Tobias P. Loka, Jakob M. Schulze, Andreas Andrusch, Jeanette Klenner, Piotr Wojciech Dabrowski, Martin S. Lindner, Andreas Nitsche, Bernhard Y. Renard
2018 bioRxiv   pre-print
We adapted the core algorithm of HiLive, a real-time read mapper, and enhanced its accuracy for our use case.  ...  We designed and implemented PathoLive, a real-time diagnostics pipeline which allows the detection of pathogens from clinical samples up to several days before the sequencing procedure is even finished  ...  Based on these k-mer positions, the q-gram lemma is applied to decide whether a certain k-mer position will be used to create, extend or discard an alignment candidate, referred to as seed [56] .  ... 
doi:10.1101/402370 fatcat:yjgnsnyhkbfidd5ad7m52kixpe

Metagenomic Sequencing and Quantitative Real-Time PCR for Fecal Pollution Assessment in an Urban Watershed

Kyle D. Brumfield, Joseph A. Cotruvo, Orin C. Shanks, Mano Sivaganesan, Jessica Hey, Nur A. Hasan, Anwar Huq, Rita R. Colwell, Menu B. Leddy
2021 Frontiers in Water  
Whole metagenome sequencing (WMS), quantitative real-time PCR (qPCR), and culture-based FIB tests were performed in an urban watershed before and after a rainfall event to determine the feasibility and  ...  Host-associated qPCR and metagenomic DNA sequencing are complementary methods for FIB monitoring that can provide enhanced understanding of microbial communities and sources of fecal pollution.  ...  of unique organism-specific k-mers annotated by each database relative to the total number of unique sequencing reads generated for that sample.  ... 
doi:10.3389/frwa.2021.626849 pmid:34263162 pmcid:PMC8274573 fatcat:gpxjzmm2dzdqfgd6hihwdywnvi

Metagenomics [chapter]

Torsten Thomas, Jack Gilbert, Folker Meyer
2014 The Role of Bioinformatics in Agriculture  
This review summarizes the current opinions in metagenomics, and provides practical guidance and advice on sample processing, sequencing technology, assembly, binning, annotation, experimental design,  ...  Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms.  ...  Alternatively, the metagenomic sequence mix can be partition into "species bins" via k-mer binning (Titus Brown, personal communications).  ... 
doi:10.1201/b16568-16 fatcat:ivdthvmv4fdjtmbjbfikulb4pe

Lightweight compositional analysis of metagenomes with FracMinHash and minimum metagenome covers [article]

Luiz Carlos Irber, Phillip T Brooks, Taylor E Reiter, N Tessa Pierce-Ward, Mahmudur Rahman Hera, David Koslicki, C. Titus Brown
2022 bioRxiv   pre-print
We next frame shotgun metagenome compositional analysis as the problem of finding a minimum collection of reference genomes that "cover" the known k-mers in a metagenome, a minimum set cover problem.  ...  Finally, we show that the minimum metagenome cover can be used to guide the selection of reference genomes for read mapping. sourmash is available as open source software under the BSD 3-Clause license  ...  LCA-based approaches such as Kraken label individual k-mers based on taxonomic lineages in a database, and then use the resulting database of annotated k-mers to assign taxonomy to reads.  ... 
doi:10.1101/2022.01.11.475838 fatcat:qr2hee27hnbwdme5b7ch2wrody

Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes

Mingjie Wang, Thomas G. Doak, Yuzhen Ye
2015 Genome Biology  
Comparative metagenomics remains challenging due to the size and complexity of metagenomic datasets.  ...  Further, its application to type 2 diabetes (T2D) metagenomic datasets reveals clear signatures of the T2D gut microbiome, revealing new phylogenetic and functional features of the gut microbial communities  ...  the k-mer ratio threshold used in the subtractive assembly, are changed ( Fig. 1 ; for real metagenomes, we used an iterative subtractive assembly approach without fixing the k-mers ratiosee below).  ... 
doi:10.1186/s13059-015-0804-0 pmid:26527161 pmcid:PMC4630832 fatcat:3jqhmgijbvfznc6oxun7pah754

Identifying Core Operons in Metagenomic Data [article]

Xiao Hu, Iddo Friedberg
2019 bioRxiv   pre-print
We tested POEM using several different assemblers on a simulated metagenome, and we show it to be highly accurate.  ...  We also demonstrate its use on a human gut metagenome sample, and discover a putative new operon.  ...  Figure 5 about here.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 2 A. k-mer-position matrix construction, shown with a 2-mer example (POEM uses 3-mer).  ... 
doi:10.1101/2019.12.20.885269 fatcat:inygkg2v2fal3kvoyozpvbs4ge

Machine learning for metagenomics: methods and tools

Hayssam Soueidan, Macha Nikolski
2017 Metagenomics  
AbstractOwing to the complexity and variability of metagenomic studies, modern machine learning approaches have seen increased usage to answer a variety of question encompassing the full range of metagenomic  ...  For each of these problems, we identify the most prominent methods, summarize the machine learning approaches used and put them into perspective of similar methods.We conclude our review looking further  ...  Acknowledgement: The authors would like to thank the anonymous reviewers for their helpful comments. This work was partly supported by Région Aquitaine grant 2014.  ... 
doi:10.1515/metgen-2016-0001 fatcat:ggs23tisyveexfmbmeg3pp5anu

Exploration and retrieval of whole-metagenome sequencing samples [article]

Sohan Seth, Niko Välimäki, Samuel Kaski, Antti Honkela
2014 arXiv   pre-print
We apply a distributed string mining framework to efficiently extract all informative sequence k-mers from a pool of metagenomic samples and use them to measure the dissimilarity between two samples.  ...  Over the recent years, the field of whole metagenome shotgun sequencing has witnessed significant growth due to the high-throughput sequencing technologies that allow sequencing genomic samples cheaper  ...  Acknowledgement The authors would like to thank Ahmed Sobih for his help with the MetaPhlAn experiments on MetaHIT and T2D-P2.  ... 
arXiv:1308.6074v2 fatcat:dfc23bbfvncx5g3rnjourueani

A Primer on Metagenomics

John C. Wooley, Adam Godzik, Iddo Friedberg, Philip E. Bourne
2010 PLoS Computational Biology  
Although metagenomics is a relative newcomer to science, the past few years have seen an explosion in computational methods applied to metagenomic-based research.  ...  Finally, the last section of this article provides a few representative studies illustrating different facets of recent scientific discoveries made using metagenomics.  ...  We would also like to thank the referees for contributing their time and effort towards making this a better article. IF dedicates his contribution to the memory of Ilan Friedberg.  ... 
doi:10.1371/journal.pcbi.1000667 pmid:20195499 pmcid:PMC2829047 fatcat:ykwqb3r4preo7is4vcqlk2caey

Exploiting topic modeling to boost metagenomic reads binning

Ruichang Zhang, Zhanzhan Cheng, Jihong Guan, Shuigeng Zhou
2015 BMC Bioinformatics  
Results: In this paper, we propose a new method TM-MCluster for binning metagenomic reads. First, we represent each metagenomic read as a set of "k-mers" with their frequencies occurring in the read.  ...  The assignment of these metagenomic reads into different species or taxonomical classes is a vital step for metagenomic analysis, which is referred to as binning of metagenomic data.  ...  So we use 4-mers to represent metagenomic reads for binning. Concretely, we slide a window of length 4 to count the frequency of each k-mer in a read.  ... 
doi:10.1186/1471-2105-16-s5-s2 pmid:25859745 pmcid:PMC4402587 fatcat:alukqr5r2zd7xjyhyqcw3pbs5e

Metagenomic binning through low density hashing [article]

Yunan Luo, Y. William Yu, Jianyang Zeng, Bonnie Berger, Jian Peng
2017 bioRxiv   pre-print
Additionally, the family of hash functions Opal uses can be generalized to other sequence analysis tasks that rely on k-mer based methods to encode long-range dependencies.  ...  Our Opal method introduces low-density, even-coverage hashing to bioinformatics applications, enabling quick and accurate metagenomic binning.  ...  We thank Moran Yassour for introducing us to the subspecies classification problem and Ashwin Narayan for fruitful discussions.  ... 
doi:10.1101/133116 fatcat:nnbcxflhl5e27lgsdy24w3etcy

Assemble CRISPRs from metagenomic sequencing data

Jikai Lei, Yanni Sun
2016 Bioinformatics  
It employs properties of CRISPRs to decompose generic assembly into local assembly. We tested it on both mock and real metagenomic data and benchmarked the performance with state-of-the-art tools.  ...  The fast accumulation of metagenomic data, which contains DNA sequences of microbial species from natural samples, provides a unique opportunity for CRISPR annotation in uncultivable microbial species.  ...  Acknowledgements We would like to thank Jiarong Guo and Dr. James Tiedje for providing us the soil data. We thank Dr. Pallavi Singh and Dr.  ... 
doi:10.1093/bioinformatics/btw456 pmid:27587670 fatcat:mzzakf74bfgkbcg53ue4mavm6e

Illumina Sequencing Artifacts Revealed by Connectivity Analysis of Metagenomic Datasets [article]

Adina Chuang Howe, Jason Pell, Rosangela Canino-Koning, Rachel Mackelprang, Susannah Tringe, Janet Jansson, James M. Tiedje, C. Titus Brown
2012 arXiv   pre-print
The removal of these sequences prior to assembly results in similar assembly content for most metagenomes and enables the use of graph partitioning to decrease assembly memory and time requirements.  ...  Specifically, we identify highly connected sequences which join a large proportion of reads within each real metagenome.  ...  If the same k-mers were consistently identified in other graph traversals, up to five times, the k-mer was flagged as a highly connected sequence.  ... 
arXiv:1212.0159v1 fatcat:3synueyyrzgghjtl5ng2wx4hde

Exploration and retrieval of whole-metagenome sequencing samples

Sohan Seth, Niko Välimäki, Samuel Kaski, Antti Honkela
2014 Bioinformatics  
We apply a distributed string mining framework to efficiently extract all informative sequence k-mers from a pool of metagenomic samples and use them to measure the dissimilarity between two samples.  ...  Motivation: Over the recent years, the field of whole-metagenome shotgun sequencing has witnessed significant growth owing to the high-throughput sequencing technologies that allow sequencing genomic samples  ...  Part of the calculations presented above was performed using computer resources within the Aalto University School of Science 'Science-IT' project.  ... 
doi:10.1093/bioinformatics/btu340 pmid:24845653 pmcid:PMC4230234 fatcat:7wnpuyedlnbgrgugb7mdqrlgdu
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