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Fast and sensitive taxonomic assignment to metagenomic contigs
2021
Bioinformatics
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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]
2020
bioRxiv
pre-print
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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
2017
Briefings in Bioinformatics
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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
2011
Standards in Genomic Sciences
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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
2017
Zenodo
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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
2015
BMC Bioinformatics
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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
2020
Microbiome
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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]
2014
arXiv
pre-print
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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
2006
Nature Methods
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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]
2019
bioRxiv
pre-print
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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
2019
BMC Genomics
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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
2019
Frontiers in Microbiology
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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]
2019
bioRxiv
pre-print
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/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
2008
BMC Genomics
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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
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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
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