Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.

scientific article published on 21 September 2017

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers. is …
instance of (P31):
scholarly articleQ13442814

External links are
P6179Dimensions Publication ID1091875834
P356DOI10.1186/S13059-017-1299-7
P932PMC publication ID5609029
P698PubMed publication ID28934964

P50authorRita R. ColwellQ3433234
Rachid OunitQ41048300
Christopher E. MasonQ88306004
Alexa B R McIntyreQ88611992
Ebrahim AfshinnekooQ93040117
P2093author name stringShawn Levy
Nur A Hasan
Stefano Lonardi
Robert J Prill
Elizabeth Hénaff
Scott Tighe
Jonathan Foox
Poorani Subramanian
Nick Greenfield
Noah Alexander
Sofia Ahsanuddin
Gail L Rosen
David Danko
Kelly Moffat
Samuel S Minot
P2860cites workThe distribution, diversity, and importance of 16S rRNA gene introns in the order ThermoprotealesQ21092846
Reagent and laboratory contamination can critically impact sequence-based microbiome analysesQ21146690
Using mobile sequencers in an academic classroomQ24286930
Gapped BLAST and PSI-BLAST: a new generation of protein database search programsQ24545170
Wisdom of crowds for robust gene network inferenceQ24604615
Integrative analysis of environmental sequences using MEGAN4Q24604814
Pyrosequencing enumerates and contrasts soil microbial diversityQ24616826
A human gut microbial gene catalogue established by metagenomic sequencingQ24618931
MEGAN analysis of metagenomic dataQ24673516
16S ribosomal DNA amplification for phylogenetic studyQ24681548
Climate variability and change in the United States: potential impacts on water- and foodborne diseases caused by microbiologic agentsQ24815196
Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosisQ27342229
Complete genome sequence of the myxobacterium Sorangium cellulosumQ28255183
A vision for ubiquitous sequencingQ28268019
Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York CityQ28595670
Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditionsQ28649887
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatmentQ28710518
Scaling laws predict global microbial diversityQ28748186
Fast and sensitive protein alignment using DIAMONDQ29011988
Avoiding Pandemic Fears in the Subway and Conquering the PlatypusQ30395119
Polar Marine Microorganisms and Climate Change.Q31135684
Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence dataQ31140088
Towards a rigorous assessment of systems biology models: the DREAM3 challengesQ33534661
A catalog of reference genomes from the human microbiomeQ33583040
Kraken: ultrafast metagenomic sequence classification using exact alignmentsQ33742022
Reducing assembly complexity of microbial genomes with single-molecule sequencingQ33742535
Strain, clone and species: comments on three basic concepts of bacteriologyQ33911372
Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipientsQ34042462
Actionable diagnosis of neuroleptospirosis by next-generation sequencingQ34053612
The Earth Microbiome project: successes and aspirationsQ34076643
NBC update: The addition of viral and fungal databases to the Naïve Bayes classification toolQ34147138
ART: a next-generation sequencing read simulator.Q34243055
A comparative evaluation of sequence classification programsQ34265338
Quikr: a method for rapid reconstruction of bacterial communities via compressive sensingQ34352277
Scalable metagenomic taxonomy classification using a reference genome databaseQ34355671
NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic readsQ34433963
CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers.Q34471973
Higher classification sensitivity of short metagenomic reads with CLARK-S.Q34537856
A metagenomic framework for the study of airborne microbial communitiesQ35069818
Accurate read-based metagenome characterization using a hierarchical suite of unique signaturesQ35656712
Scaffolding of a bacterial genome using MinION nanopore sequencingQ35684645
Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities.Q35832785
Comparative metagenomics reveals impact of contaminants on groundwater microbiomesQ35845988
The microbiome quality control project: baseline study design and future directionsQ35865351
Human milk microbiota profiles in relation to birthing method, gestation and infant genderQ35887554
An evaluation of the accuracy and speed of metagenome analysis toolsQ35896599
Strain-level microbial epidemiology and population genomics from shotgun metagenomicsQ35964692
WEVOTE: Weighted Voting Taxonomic Identification Method of Microbial SequencesQ36147538
Geospatial Resolution of Human and Bacterial Diversity with City-Scale MetagenomicsQ36295913
Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP)Q36321389
ConStrains identifies microbial strains in metagenomic datasetsQ36364571
Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strainsQ36860756
Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genomeQ37238362
Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the EnvironmentQ37349245
Scaffolding and completing genome assemblies in real-time with nanopore sequencingQ37660635
Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of deliveryQ37693667
International Standards for Genomes, Transcriptomes, and MetagenomesQ37713218
Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencingQ38368749
PhyloSift: phylogenetic analysis of genomes and metagenomesQ41882289
Unexplored Archaeal Diversity in the Great Ape Gut Microbiome.Q41911619
Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.Q41926823
Lack of Evidence for Plague or Anthrax on the New York City SubwayQ48032597
Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics softwareQ57179882
MetaPhlAn2 for enhanced metagenomic taxonomic profilingQ57255766
Scaffolding and Completing Genome Assemblies in Real-time with Nanopore SequencingQ57765361
P433issue1
P921main subjectmetagenomicsQ903778
P304page(s)182
P577publication date2017-09-21
P1433published inGenome BiologyQ5533480
P1476titleComprehensive benchmarking and ensemble approaches for metagenomic classifiers
P478volume18

Reverse relations

cites work (P2860)
Q90260951A Black Death mass grave at Thornton Abbey: the discovery and examination of a fourteenth-century rural catastrophe
Q57478236A Metagenomic Approach to Evaluating Surface Water Quality in Haiti
Q55514196A space and time-efficient index for the compacted colored de Bruijn graph.
Q56888318Analysis of sequencing strategies and tools for taxonomic annotation: Defining standards for progressive metagenomics
Q55396894BLAST-based validation of metagenomic sequence assignments.
Q92525232Benchmarking Metagenomics Tools for Taxonomic Classification
Q90544829Benchmarking the MinION: Evaluating long reads for microbial profiling
Q94450938CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data
Q96230972Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
Q92659409Clinical metagenomics
Q91281789Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications
Q89980627Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability
Q64072314Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers
Q94457674Crewmember microbiome may influence microbial composition of ISS habitable surfaces
Q99237749Enhanced Detection of DNA Viruses in the Cerebrospinal Fluid of Encephalitis Patients Using Metagenomic Next-Generation Sequencing
Q89724850Enteric Virome and Carcinogenesis in the Gut
Q56890690Fine-scale differentiation between and group signatures in metagenome shotgun data
Q89561552Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines
Q90371594Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample
Q97542113IDMIL: an alignment-free Interpretable Deep Multiple Instance Learning (MIL) for predicting disease from whole-metagenomic data
Q100562495IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring
Q60921022Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies
Q90270797Improved Metagenomic Taxonomic Profiling Using a Curated Core Gene-Based Bacterial Database Reveals Unrecognized Species in the Genus Streptococcus
Q59330586KrakenUniq: confident and fast metagenomics classification using unique k-mer counts
Q90064938Large scale microbiome profiling in the cloud
Q97070200MARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding
Q64080144MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs
Q97542057MetaBCC-LR: metagenomics binning by coverage and composition for long reads
Q60928269Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children
Q60922635Minerva: an alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics
Q92783846Oropharyngeal microbiome of a college population following a meningococcal disease outbreak
Q54217638Overview of Virus Metagenomic Classification Methods and Their Biological Applications.
Q90412962Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA
Q47382973Phage hunters: Computational strategies for finding phages in large-scale 'omics datasets.
Q97542472Phylogenetic double placement of mixed samples
Q92300617Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance
Q101476605Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids
Q58095216RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification
Q57094607Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research
Q64075192Signal enrichment with strain-level resolution in metagenomes using topological data analysis
Q64114216Systematic benchmarking of omics computational tools
Q56892351The Microbe Directory: An annotated, searchable inventory of microbes' characteristics
Q64054493Ultra-deep, long-read nanopore sequencing of mock microbial community standards
Q97542044ganon: precise metagenomics classification against large and up-to-date sets of reference sequences
Q52626821taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable time.

Search more.