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Assessing taxonomic metagenome profilers with OPAL

https://doi.org/10.1101/372680
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/j.1538-7305.1948.tb01338.xopenalex-snapshot
A Mathematical Theory of Communication
inferredcites →https://doi.org/10.1007/s00248-014-0559-2openalex-snapshot
Soil-Borne Microbiome: Linking Diversity to Function
inferredcites →https://doi.org/10.1007/s00285-018-1235-9openalex-snapshot
EMDUniFrac: exact linear time computation of the UniFrac metric and identification of differentially abundant organisms
inferredcites →https://doi.org/10.1038/ijo.2017.66openalex-snapshot
Gut microbiome diversity and high-fibre intake are related to lower long-term weight gain
inferredcites →https://doi.org/10.1038/nmeth.2066openalex-snapshot
Metagenomic microbial community profiling using unique clade-specific marker genes
inferredcites →https://doi.org/10.1038/nmeth.2693openalex-snapshot
Metagenomic species profiling using universal phylogenetic marker genes
inferredcites →https://doi.org/10.1038/nmeth.4458openalex-snapshot
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
inferredcites →https://doi.org/10.1038/s41598-017-10382-2openalex-snapshot
Omega-3 fatty acids correlate with gut microbiome diversity and production of N-carbamylglutamate in middle aged and elderly women
inferredcites →https://doi.org/10.1038/srep19233openalex-snapshot
An evaluation of the accuracy and speed of metagenome analysis tools
inferredcites →https://doi.org/10.1073/pnas.1215210110openalex-snapshot
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
inferredcites →https://doi.org/10.1093/bioinformatics/16.5.412openalex-snapshot
Assessing the accuracy of prediction algorithms for classification: an overview
inferredcites →https://doi.org/10.1093/bioinformatics/btt077openalex-snapshot
Protein signature-based estimation of metagenomic abundances including all domains of life and viruses
inferredcites →https://doi.org/10.1093/bioinformatics/btt086openalex-snapshot
QUAST: quality assessment tool for genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btt336openalex-snapshot
Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing
inferredcites →https://doi.org/10.1093/bioinformatics/btu320openalex-snapshot
SEK: sparsity exploiting k-mer-based estimation of bacterial community composition
inferredcites →https://doi.org/10.1093/bioinformatics/btu721openalex-snapshot
TIPP: taxonomic identification and phylogenetic profiling
inferredcites →https://doi.org/10.1093/bioinformatics/btv697openalex-snapshot
MetaQUAST: evaluation of metagenome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btw150openalex-snapshot
DUDes: a top-down taxonomic profiler for metagenomics
inferredcites →https://doi.org/10.1093/gigascience/giy069openalex-snapshot
AMBER: Assessment of Metagenome BinnERs
inferredcites →https://doi.org/10.1101/300970openalex-snapshot
CAMISIM: Simulating metagenomes and microbial communities
inferredcites →https://doi.org/10.1111/j.1467-9868.2011.01018.xopenalex-snapshot
The Phylogenetic Kantorovich–Rubinstein Metric for Environmental Sequence Samples
inferredcites →https://doi.org/10.1128/aem.71.12.8228-8235.2005openalex-snapshot
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
inferredcites →https://doi.org/10.1128/msystems.00020-16openalex-snapshot
MetaPalette: a k -mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation
inferredcites →https://doi.org/10.1186/1471-2164-12-s2-s4openalex-snapshot
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
inferredcites →https://doi.org/10.1186/2047-217x-1-7openalex-snapshot
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
inferredcites →https://doi.org/10.1186/s12864-015-1419-2openalex-snapshot
CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
inferredcites →https://doi.org/10.1186/s13742-015-0087-0openalex-snapshot
Bioboxes: standardised containers for interchangeable bioinformatics software
inferredcites →https://doi.org/10.1186/s40168-019-0633-6openalex-snapshot
CAMISIM: simulating metagenomes and microbial communities
inferredcites →https://doi.org/10.1371/journal.pone.0131080openalex-snapshot
Biodiversity on the Rocks: Macrofauna Inhabiting Authigenic Carbonate at Costa Rica Methane Seeps
inferredcites →https://doi.org/10.1371/journal.pone.0140644openalex-snapshot
ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition
inferredcites →https://doi.org/10.18637/jss.v059.i10openalex-snapshot
Tidy Data
inferredcites →https://doi.org/10.2307/1218190openalex-snapshot
EVOLUTION AND MEASUREMENT OF SPECIES DIVERSITY
inferredcites →https://doi.org/10.5524/100344openalex-snapshot
Benchmark data sets, software results and reference data for the first CAMI challenge.
inferredcites →https://doi.org/10.7717/peerj.425openalex-snapshot
FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41467-019-08844-4openalex-snapshot
Microbial abundance, activity and population genomic profiling with mOTUs2
inferred← citeshttps://doi.org/10.1101/2024.02.12.580015openalex-snapshot
Memory-bound k -mer selection for large and evolutionary diverse reference libraries
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