Filters








1,205 Hits in 3.9 sec

Fast and sensitive taxonomic assignment to metagenomic contigs

M Mirdita, M Steinegger, F Breitwieser, J Söding, E Levy Karin
2021 Bioinformatics  
MMseqs2 taxonomy is a new tool to assign taxonomic labels to metagenomic contigs.  ...  It extracts all possible protein fragments from each contig, quickly retains those that can contribute to taxonomic annotation, assigns them with robust labels and determines the contig's taxonomic identity  ...  ., 2013) strategy to assign translated fragments to taxonomic nodes (Supp. Inf.).  ... 
doi:10.1093/bioinformatics/btab184 pmid:33734313 pmcid:PMC8479651 fatcat:4jna6neswbhene5zqjy7skm6iq

Fast and sensitive taxonomic assignment to metagenomic contigs [article]

Milot Mirdita, Martin Steinegger, Florian Breitwieser, Johannes Soeding, Eli Levy Karin
2020 bioRxiv   pre-print
MMseqs2 taxonomy is a new tool to assign taxonomic labels to metagenomic contigs.  ...  It extracts all possible protein fragments from each contig, quickly retains those that can contribute to taxonomic annotation, assigns them with robust labels and determines the contig's taxonomic identity  ...  While most methods label short metagenomic reads (reviewed in [11] ), only a handful (e.g. [6] ) assign entire contigs, even though this should lead to improved accuracy.  ... 
doi:10.1101/2020.11.27.401018 fatcat:vp7mdp32a5eo5nb5fj3zb6rsii

A review of methods and databases for metagenomic classification and assembly

Florian P. Breitwieser, Jennifer Lu, Steven L. Salzberg
2017 Briefings in Bioinformatics  
His research interests include metagenomics classification and visualization methods and their application to infectious disease diagnosis.  ...  His laboratory conducts research on DNA and RNA sequence analysis including genome assembly, transcriptome assembly, sequence alignment and metagenomics.  ...  The assignment can then be made with fast, sensitive aligners, such as Bowtie2 [85] used by MetaPhlAn and HMMER [86] used by Phylosift [87] and mOTU [82] .  ... 
doi:10.1093/bib/bbx120 pmid:29028872 fatcat:lpy4gbxtyzdb5jyz7bh2zdz7iq

ClaMS: A Classifier for Metagenomic Sequences

Amrita Pati, Lenwood S. Heath, Nikos C. Kyrpides, Natalia Ivanova
2011 Standards in Genomic Sciences  
Introduction Metagenome binning is the process of assigning nucleotide sequences in a metagenome to known taxonomic groups.  ...  Mapping sequences to their taxonomic groups of origin leads to better characterization of a metagenome, which facilitates the accomplishment of objectives such as genome assembly from metagenomes and assembly  ... 
doi:10.4056/sigs.2075298 pmid:22180827 pmcid:PMC3235515 fatcat:5zuwsyhhpjcm7ci5oqejf5itea

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.  ...  and the microbial community. | Our first method, taxator-tk, assigns nucleotide sequences from metagenomes to corresponding taxa and approaches two challenges: the precise prediction of taxa and the application  ...  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

RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets

Matthias Scheuch, Dirk Höper, Martin Beer
2015 BMC Bioinformatics  
RIEMS assigns every individual read sequence within a dataset taxonomically by cascading different sequence analyses with decreasing stringency of the assignments using various software applications.  ...  Conclusions: RIEMS has the potential to fill the gap that still exists with regard to data analysis for metagenomics studies.  ...  Acknowledgements We are indebted to Moctezuma Reimann for excellent technical assistance.  ... 
doi:10.1186/s12859-015-0503-6 pmid:25886935 pmcid:PMC4351923 fatcat:yvoadiaqd5hg7mbjxalspvne7e

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics

Eli Levy Karin, Milot Mirdita, Johannes Söding
2020 Microbiome  
The open-source (GPLv3) MetaEuk software (https://github.com/soedinglab/metaeuk) enables large-scale eukaryotic metagenomics through reference-based, sensitive taxonomic and functional annotation.  ...  To demonstrate MetaEuk's power to discover novel eukaryotic proteins in large-scale metagenomic data, we assembled contigs from 912 samples of the Tara Oceans project.  ...  David Burstein from Tel Aviv University for his helpful insights concerning the phylogenetic analyses and Dr.  ... 
doi:10.1186/s40168-020-00808-x pmid:32245390 fatcat:u4nzrxwblfawpm4ls2nhmtjwpa

PhyloPythiaS+: A self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes [article]

I. Gregor, J. Dröge, M. Schirmer, C. Quince, A. C. McHardy
2014 arXiv   pre-print
Metagenomics is an approach for characterizing environmental microbial communities in situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa.  ...  Assignment to low-ranking taxonomic bins is an important challenge for binning methods as is scalability to Gb-sized datasets generated with deep sequencing techniques.  ...  PPS+ was not that sensitive to this distance.  ... 
arXiv:1406.7123v1 fatcat:7xl7lwwk7bcnfarevhjsr3pmeq

Accurate phylogenetic classification of variable-length DNA fragments

Alice Carolyn McHardy, Héctor García Martín, Aristotelis Tsirigos, Philip Hugenholtz, Isidore Rigoutsos
2006 Nature Methods  
Metagenome studies have retrieved vast amounts of sequence data from a variety of environments leading to new discoveries and insights into the uncultured microbial world.  ...  A taxonomic characterization of metagenomic fragments is required for a deeper understanding of shotgunsequenced microbial communities, but success has mostly been limited to sequences containing phylogenetic  ...  Kunin and F. Warnecke for help with selection of CAP and Thiothrix-specific training sets and for validation analyses of the metagenomic data-set binning, L. Krause for providing the SEED data, T.  ... 
doi:10.1038/nmeth976 pmid:17179938 fatcat:rnx2bpv5g5eghnemqafm5n6ew4

Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes [article]

Javier Tamames, Marta Cobo-Simon, Fernando Puente-Sanchez
2019 bioRxiv   pre-print
One of the most important distinctions is the way to perform taxonomic and functional assignment, choosing between the usage of assemblies or the direct analysis of raw sequence reads instead.  ...  We have studied this point by analysing several real and mock metagenomes using different methodologies and tools, and comparing the resulting taxonomic and functional profiles.  ...  This research was funded by projects CTM2013-48292-C3-2-R and CTM2016-80095-C2-1-R, Spanish Ministry of Economy and Competitiveness.  ... 
doi:10.1101/522292 fatcat:53zd6zgvabguxhuam2re7cevsq

Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes

Javier Tamames, Marta Cobo-Simón, Fernando Puente-Sánchez
2019 BMC Genomics  
One of the most important distinctions is the way to perform taxonomic and functional assignment, choosing between the use of assembly algorithms or the direct analysis of raw sequence reads instead by  ...  We have analysed several real and mock metagenomes using different methodologies and tools, and compared the resulting taxonomic and functional profiles.  ...  Metagenomic datasets can be found in the SRA archive with accession SRP104009 (Thermal dataset), SRS052697 (Gut dataset). Ethics approval and consent to participate Not applicable.  ... 
doi:10.1186/s12864-019-6289-6 pmid:31823721 pmcid:PMC6902526 fatcat:ajjn76ne5jevngkqyg2tvwy76q

SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline

Javier Tamames, Fernando Puente-Sánchez
2019 Frontiers in Microbiology  
We were also able to co-assemble two of these metagenomes and complete the full analysis in less than one day using a simple laptop computer.  ...  It also includes binning and bin checking for retrieving individual genomes. Internal checks for the assembly and binning steps provide information about the consistency of contigs and bins.  ...  Taxonomic Assignment of Contigs and Disparity Check The taxonomic assignments of individual genes are used to produce consensus assignments for the contigs.  ... 
doi:10.3389/fmicb.2018.03349 pmid:30733714 pmcid:PMC6353838 fatcat:yjwycdt3izb4rdtylgugg4znoq

MetaEuk – sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics [article]

Eli Levy Karin, Milot Mirdita, Johannes Söding
2019 bioRxiv   pre-print
/soedinglab/metaeuk) enables large-scale eukaryotic metagenomics through reference-based, sensitive taxonomic and functional annotation.  ...  To demonstrate MetaEuk's power to discover novel eukaryotic proteins in large-scale metagenomic data, we assembled contigs from 912 samples of the Tara Oceans project.  ...  Lower values were assigned at the domain level. The predictions on each 601 contig were examined and the best-scoring one was used to confer taxonomic annotation to 602 that contig.  ... 
doi:10.1101/851964 fatcat:qtkfhftp4fauljtcxqgzvduswq

Estimating the extent of horizontal gene transfer in metagenomic sequences

Javier Tamames, Andrés Moya
2008 BMC Genomics  
The methods are based on phylogenetic and DNA compositional approaches, and have allowed us to assess the extent of possible HGT events in metagenomes for the first time.  ...  Therefore it is important to develop new methods or to adapt existing ones to be used with metagenomic sequences.  ...  Acknowledgements JT wishes to acknowledge Miguel Pignatelli for technical support, and Iakes Ezkurdia and Iñaki Comas for discussions.  ... 
doi:10.1186/1471-2164-9-136 pmid:18366724 pmcid:PMC2324111 fatcat:viq7b3malngllkvidzjhdikag4

PhyloMagnet: fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics

2019 Bioinformatics  
When applied to a group of metagenomes for which a set of metagenome assembled genomes (MAGs) have been published, we could detect the majority of the taxonomic labels that the MAGs had been annotated  ...  In a metatranscriptomic setting, the phylogenetic placement of assembled contigs corresponds to that of transcripts obtained from transcriptome assembly.  ...  In a final stage, the tool gappa is used to annotate the internal branches of the reference tree and assign taxonomic labels to the translated contigs based on the likelihood weights of the placement  ... 
doi:10.1093/bioinformatics/btz799 pmid:31647547 pmcid:PMC7703773 fatcat:vxzvwecib5hzdkowlakaraoe4m
« Previous Showing results 1 — 15 out of 1,205 results