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MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis

João F Matias Rodrigues, Thomas S B Schmidt, Janko Tackmann, Christian von Mering, Inanc Birol
2017 Bioinformatics  
MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis. Bioinformatics, 33(23):3808-3810.  ...  Results: Here we present MAPseq, a framework for reference-based rRNA sequence analysis that is up to 30% more accurate (F1 =2 score) and up to one hundred times faster than existing solutions, providing  ...  Downloaded from https://academic.oup.com/bioinformatics/article-abstract/doi/10.1093/bioinformatics/btx517/4082276/MAPseq-highly-efficient-k-mer-search-with by University of Zurich user on 05 October  ... 
doi:10.1093/bioinformatics/btx517 pmid:28961926 pmcid:PMC5860325 fatcat:uehppsz6gfdhhkguzbvbg5rdtm

MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis

João F Matias Rodrigues, Thomas Sebastian Benedikt Schmidt, Janko Tackmann, Christian Von Mering
2017
MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis. Bioinformatics, 33(23):3808-3810.  ...  Results: Here we present MAPseq, a framework for reference-based rRNA sequence analysis that is up to 30% more accurate (F1 =2 score) and up to one hundred times faster than existing solutions, providing  ...  Downloaded from https://academic.oup.com/bioinformatics/article-abstract/doi/10.1093/bioinformatics/btx517/4082276/MAPseq-highly-efficient-k-mer-search-with by University of Zurich user on 05 October  ... 
doi:10.5167/uzh-140370 fatcat:qggckzzxffazxoqzvmsr42xzfu

MAPseq: Improved Speed, Accuracy And Consistency In Ribosomal RNA Sequence Analysis [article]

Joao F Matias Rodrigues, Thomas SB Schmidt, Janko Tackmann, Christian von Mering
2017 bioRxiv   pre-print
Here we present MAPseq, a framework for reference-based rRNA metagenomic analysis that is up to 30% more accurate (F1/2 score) and up to one hundred times faster than existing solutions, providing in a  ...  single run multiple taxonomy classifications and hierarchical OTU mappings, for both amplicon and shotgun sequencing strategies, and for datasets of virtually any size.  ...  effect on consistency, and UCLUST was clearly outperformed on both, by MAPseq mapping and by AL clustering.  ... 
doi:10.1101/126953 fatcat:cxbphgqeafgj3ges57hpyskxqm

ELIXIR-EXCELERATE D6.3: Report describing a set of tools, pipelines and search engine for interrogation of marine metagenomic data

Alex Mitchell, Maxim Scheremetjew, Gianluca De Moro, Bruno Fosso, Monica Santamaria, Graziano Pesole, Shriya Raj, Lars Ailo Bongo, Nils Peder Willassen, Robert D. Finn
2019 Zenodo  
. ● Examples generated for federating searches across resource programmatic interfaces. ● Wide range of different training activities and material developed. ● Major interaction with Compute (WP4) and  ...  ● Pipelines expanded to increase scope of analysis, tools updated and tailoring of analysis to meet the demands of the Marine Metagenomics community. ● Analysis pipelines described in the Common Workflow  ...  While this is a suboptimal solution, in the longer term, the inclusion in MGnify of either a K-mer based mechanism for taxonomic profiling, or the use of protein matches against a reference database as  ... 
doi:10.5281/zenodo.3228301 fatcat:nb2r64odubauno62doau6n5lr4

Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets [article]

Isabel F Escapa, Yanmei Huang, Tsute Chen, Maoxuan Lin, Alexis Kokaras, Floyd E Dewhirst, Katherine P Lemon
2019 bioRxiv   pre-print
In addition, we overcame technical limitations to successfully use Illumina sequences for the 16S rRNA gene V1-V3 region, the most informative segment for classifying bacteria native to the human aerodigestive  ...  We also generated a full-length eHOMD 16S rRNA gene training set, which we used in conjunction with an independent PacBio Single Molecule, Real-Time (SMRT)-sequenced sinonasal dataset to validate the representation  ...  Matias Rodrigues JF, Schmidt TSB, Tackmann J, von Mering C: MAPseq: highly 837 efficient k-mer search with confidence estimates, for rRNA sequence 838 analysis.  ... 
doi:10.1101/791574 fatcat:ajcufzy3araydklfd3ej46ai6e

DAIRYdb: A manually curated gold standard reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products [article]

Marco Meola, Etienne Rifa, Noam Shani, Celine Delbes, Helene Berthoud, Christophe Chassard
2018 bioRxiv   pre-print
We provide a manually curated database composed of 10'290 full-length 16S rRNA gene sequences from prokaryotes tailored for dairy products analysis (https://github.com/marcomeola/DAIRYdb).  ...  Taxonomy annotation in universal 16S databases with environmental sequences like Silva, RDP or Greengenes is based on predictions rather than on studies of type strains or isolates.  ...  ACKNOWLEDGEMENTS Eric Dugat-Bony (INRA Grignon, GMPA) improved the completeness of the DAIRYdb by providing some additional 16S sequences from his own studies related to cheese rind bacteria.  ... 
doi:10.1101/386151 fatcat:o5tl5ooidzhqzbvjqoxq5o6iza

Diel Protein Regulation of Marine Picoplanktonic Communities Assessed by Metaproteomics

Augustin Géron, Johannes Werner, Philippe Lebaron, Ruddy Wattiez, Sabine Matallana-Surget
2021 Microorganisms  
This study unravels, for the first time, the diel variation in the protein expression of major free-living and particle-attached microbial players at the sea surface, totaling an analysis of eight metaproteomes  ...  Our results showed similar taxonomic distribution of free-living and particle-attached bacterial populations, with Alphaproteobacteria, Gammaproteobacteria and Cyanobacteria being the most active members  ...  MAPseq: Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis. Bioinformatics 2017, 33, 3808–3810. [CrossRef] 42. Buchfink, B.; Xie, C.; Huson, D.H.  ... 
doi:10.3390/microorganisms9122621 pmid:34946222 pmcid:PMC8707726 fatcat:7vu5wifk75bsjmpxzttupiztny

Novel Computational Techniques For Mapping And Classifying Next-Generation Sequencing Data

Karel Břinda, Gregory Kucherov, Valentina Boeva
2016 Zenodo  
In this thesis, we present novel computational techniques for read mapping and taxonomic classification. With more than a hundred of published mappers, read mapping might be considered fully solved.  ...  Beyond its application to dynamic mapping, Ococo can be employed as an online SNP caller in various analysis pipelines, enabling SNP calling from a stream without savi [...]  ...  The tool is easy to use and highly efficient, with memory footprint of approximately 60 GB for a database of 2,300 bacterial genomes.  ... 
doi:10.5281/zenodo.1045317 fatcat:agbwpocisncwvihn2ij5q3ongq

Identification of gut microbiome markers for schizophrenia delineates a potential role of Streptococcus [article]

Feng Zhu, Yanmei Ju, Wei Wang, Qi Wang, Ruijin Guo, Qingyan Ma, Qiang Sun, Yajuan Fan, Yuying Xie, Zai Yang, Zhuye Jie, Binbin Zhao (+6 others)
2019 bioRxiv   pre-print
Here, we characterized the gut microbiota in schizophrenia using shotgun metagenomic sequencing of feces from a discovery cohort of 90 drug free patients and 81 controls, as well as a validation cohort  ...  In conclusion, our study identified 26 schizophrenia associated bacterial species representing potential microbial targets for future treatment, as well as GBMs, some of which may give rise to new microbial  ...  MAPseq: highly efficient 553 k-mer search with confidence estimates, for rRNA sequence analysis. Bioinformatics 33, 554 3808-3810 (2017). 555 34. Lloyd-Price, J., et al.  ... 
doi:10.1101/774265 fatcat:h7is3yphercfzmhym3fqd2bche

Wiring the Microbial Web of Earth – New Approaches for Scalable Computational Prediction of Interpretable Microbial Ecosystem Structure

Janko Tackmann
2019
Such workflows employ for instance diversity-based comparisons of community profiles or the identification of community members that are strongly associated with a condition of interest (e.g. a disease  ...  However, these approaches typically do not account for a variety of artifacts, including for instance shared ecological and environmental dependencies.  ...  Availability of data and materials Short read sequencing data used for GlobalBodysites can be downloaded from the NCBI Sequencing Read Archive database [29] using the accession numbers provided in Additional  ... 
doi:10.5167/uzh-189835 fatcat:vqsodeuzvfalzfatui4pyk2hxm

The MGX framework for microbial community analysis

Sebastian Jaenicke
2020
Acknowledgements Alexander Goesmann and Jens Stoye are acknowledged for the opportunity and supervision of this PhD thesis.  ...  I'm also grateful to Peter Belmann and Patrick Blumenkamp for the contribution of software components which they developed during their B.Sc. and M.Sc. theses under my supervision.  ...  DNA sequences is performed employing two different tools; initially, a k-mer-based classification algorithm (Kraken) is applied, and for sequences that remain unassigned, a sequence homology search based  ... 
doi:10.4119/unibi/2940338 fatcat:ef3zg6nqlrhdzm4ysj533576ee

High-throughput sequencing with thermostable group II intron reverse transcriptases

Ching Kai Douglas Wu, 0000-0001-6179-3110, Austin, The University Of Texas At, Alan Lambowitz
2020
RNA sequencing libraries for the Illumina short-read sequencing platform.  ...  Using RNA sequencing data generated with this novel class of reverse transcriptase, I also showed that current state-of-the-art bioinformatic tools were not optimal for analyzing all RNA classes and biasing  ...  We reason that a relatively large k-mer size and erroneous sequencing reads likely impede matching to the indexed transcriptome even when these sequencing reads are shredded into k-mers, since all k-mers  ... 
doi:10.26153/tsw/9478 fatcat:3kpiytwt6bfe5oa2uvgbyofpgy