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Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies

https://doi.org/10.1101/202077

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What this work says

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

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Consistency and inconsistency in network meta‐analysis: concepts and models for multi‐arm studies

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Network meta‐analysis, electrical networks and graph theory

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[4] Use of External Controls in Microarray Experiments

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High-resolution phylogenetic microbial community profiling

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The self‐assessment trap: can we all be better than average?

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Unusual biology across a group comprising more than 15% of domain Bacteria

inferredcites →https://doi.org/10.1038/nbt.2676openalex-snapshot

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

inferredcites →https://doi.org/10.1038/nbt.3935openalex-snapshot

Shotgun metagenomics, from sampling to analysis

inferredcites →https://doi.org/10.1038/nmeth.3589openalex-snapshot

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

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DADA2: High-resolution sample inference from Illumina amplicon data

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/nmeth.f.303openalex-snapshot

QIIME allows analysis of high-throughput community sequencing data

inferredcites →https://doi.org/10.1038/nmeth0311-191openalex-snapshot

Taxonomic metagenome sequence assignment with structured output models

inferredcites →https://doi.org/10.1038/nmeth0511-367openalex-snapshot

PhymmBL expanded: confidence scores, custom databases, parallelization and more

inferredcites →https://doi.org/10.1038/nrg3182openalex-snapshot

The human microbiome: at the interface of health and disease

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Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis

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Next generation sequencing data of a defined microbial mock community

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An evaluation of the accuracy and speed of metagenome analysis tools

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Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

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Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

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Comparative analysis of ribonuclease P RNA using gene sequences from natural microbial populations reveals tertiary structural elements.

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Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes

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A review of methods and databases for metagenomic classification and assembly

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Rose: generating sequence families.

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Over-optimism in bioinformatics research

inferredcites →https://doi.org/10.1093/bioinformatics/btq230openalex-snapshot

Classification of DNA sequences using Bloom filters

inferredcites →https://doi.org/10.1093/bioinformatics/btq323openalex-snapshot

Over-optimism in bioinformatics: an illustration

inferredcites →https://doi.org/10.1093/bioinformatics/btq619openalex-snapshot

NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads

inferredcites →https://doi.org/10.1093/bioinformatics/btr708openalex-snapshot

ART: a next-generation sequencing read simulator

inferredcites →https://doi.org/10.1093/bioinformatics/btt389openalex-snapshot

Scalable metagenomic taxonomy classification using a reference genome database

inferredcites →https://doi.org/10.1093/bioinformatics/btu153openalex-snapshot

Prokka: rapid prokaryotic genome annotation

inferredcites →https://doi.org/10.1093/bioinformatics/btu745openalex-snapshot

Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods

inferredcites →https://doi.org/10.1093/gigascience/giy054openalex-snapshot

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments

inferredcites →https://doi.org/10.1093/molbev/msr268openalex-snapshot

ALF—A Simulation Framework for Genome Evolution

inferredcites →https://doi.org/10.1093/nar/gkq275openalex-snapshot

Ab initio gene identification in metagenomic sequences

inferredcites →https://doi.org/10.1093/nar/gkq747openalex-snapshot

FragGeneScan: predicting genes in short and error-prone reads

inferredcites →https://doi.org/10.1093/nar/gkr1067openalex-snapshot

Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering

inferredcites →https://doi.org/10.1093/nar/gkr225openalex-snapshot

Taxonomic classification of metagenomic shotgun sequences with CARMA3

inferredcites →https://doi.org/10.1093/nar/gks251openalex-snapshot

Grinder: a versatile amplicon and shotgun sequence simulator

inferredcites →https://doi.org/10.1093/nar/gks828openalex-snapshot

Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms

inferredcites →https://doi.org/10.1093/nar/gkv1322openalex-snapshot

The MG-RAST metagenomics database and portal in 2015

inferredcites →https://doi.org/10.1093/nar/gkv180openalex-snapshot

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

inferredcites →https://doi.org/10.1101/027607openalex-snapshot

One Codex: A Sensitive and Accurate Data Platform for Genomic Microbial Identification

inferredcites →https://doi.org/10.1101/092205openalex-snapshot

Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software

inferredcites →https://doi.org/10.1101/gr.213959.116openalex-snapshot

metaSPAdes: a new versatile metagenomic assembler

inferredcites →https://doi.org/10.1101/gr.5969107openalex-snapshot

MEGAN analysis of metagenomic data

inferredcites →https://doi.org/10.1109/bibm.2010.5706544openalex-snapshot

MetaPhyler: Taxonomic profiling for metagenomic sequences

inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05519.xopenalex-snapshot

Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next‐generation DNA sequencing

inferredcites →https://doi.org/10.1126/science.1107851openalex-snapshot

Comparative Metagenomics of Microbial Communities

inferredcites →https://doi.org/10.1128/aem.01541-09openalex-snapshot

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

inferredcites →https://doi.org/10.1128/mr.51.2.221-271.1987openalex-snapshot

Bacterial evolution

inferredcites →https://doi.org/10.1177/0962280207080643openalex-snapshot

Evaluation of networks of randomized trials

inferredcites →https://doi.org/10.1186/1471-2105-13-92openalex-snapshot

A comparative evaluation of sequence classification programs

inferredcites →https://doi.org/10.1186/1471-2164-15-264openalex-snapshot

Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data

inferredcites →https://doi.org/10.1186/2042-5783-2-3openalex-snapshot

Metagenomics - a guide from sampling to data analysis

inferredcites →https://doi.org/10.1186/gb-2013-14-5-r51openalex-snapshot

Characterizing and measuring bias in sequence data

inferredcites →https://doi.org/10.1186/gb-2014-15-3-r46openalex-snapshot

Kraken: ultrafast metagenomic sequence classification using exact alignments

inferredcites →https://doi.org/10.1186/s12859-015-0788-5openalex-snapshot

Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities

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/s12864-015-2063-6openalex-snapshot

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

inferredcites →https://doi.org/10.1186/s12874-017-0417-2openalex-snapshot

Towards evidence-based computational statistics: lessons from clinical research on the role and design of real-data benchmark studies

inferredcites →https://doi.org/10.1186/s13059-017-1299-7openalex-snapshot

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers

inferredcites →https://doi.org/10.1186/s40168-015-0093-6openalex-snapshot

Xander: employing a novel method for efficient gene-targeted metagenomic assembly

inferredcites →https://doi.org/10.1186/s40168-017-0233-2openalex-snapshot

Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads

inferredcites →https://doi.org/10.1186/s40168-018-0470-zopenalex-snapshot

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

inferredcites →https://doi.org/10.1371/journal.pcbi.1002358openalex-snapshot

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

inferredcites →https://doi.org/10.1371/journal.pcbi.1003737openalex-snapshot

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data

inferredcites →https://doi.org/10.1371/journal.pcbi.1004957openalex-snapshot

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

inferredcites →https://doi.org/10.1371/journal.pone.0003373openalex-snapshot

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

inferredcites →https://doi.org/10.1371/journal.pone.0039315openalex-snapshot

Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research

inferredcites →https://doi.org/10.1371/journal.pone.0041224openalex-snapshot

Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads

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A Plea for Neutral Comparison Studies in Computational Sciences

inferredcites →https://doi.org/10.1371/journal.pone.0169563openalex-snapshot

Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics

inferredcites →https://doi.org/10.3389/fpls.2014.00209openalex-snapshot

An introduction to the analysis of shotgun metagenomic data

inferredcites →https://doi.org/10.4137/bbi.s12462openalex-snapshot

Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies

inferredcites →https://doi.org/10.7717/peerj-cs.104openalex-snapshot

Bracken: estimating species abundance in metagenomics data

inferredcites →https://doi.org/10.7717/peerj.1603openalex-snapshot

PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes

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