Research graph
References from RandomReadsMG: Rapid, realistic metagenome simulation at terabase scale for benchmarking and experimental design. Local targets link to admitted publications; unresolved targets remain external evidence.
Metagenomics: genomic analysis of microbial communities
10.1146/annurev.genet.38.072902.091216 · 2004 · External reference
High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats
10.1128/mbio.02288-14 · 2015 · External reference
Synthetic data in health care: A narrative review
10.1371/journal.pdig.0000082 · 2023 · External reference
MetaSim: a sequencing simulator for genomics and metagenomics
10.1371/journal.pone.0003373 · 2008 · External reference
Simulating Illumina metagenomic data with InSilicoSeq
10.1093/bioinformatics/bty630 · 2019 · External reference
CAMISIM: simulating metagenomes and microbial communities
10.1186/s40168-019-0633-6 · 2019 · External reference
Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim
10.1093/gigascience/giad013 · 2023 · External reference
MeStanG-resource for high-throughput sequencing standard data sets generation for bioinformatic methods evaluation and validation
10.3390/biology14010069 · 2025 · External reference
MeSS and assembly_finder: a toolkit for in silico metagenomic sample generation
10.1093/bioinformatics/btae760 · 2024 · External reference
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
10.1038/nmeth1043 · 2007 · External reference
Benchmarking metagenomics tools for taxonomic classification
10.1016/j.cell.2019.07.010 · 2019 · External reference
Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit
10.1038/s41596-020-00480-3 · 2021 · External reference
Performance evaluation of six popular short-read simulators
10.1038/s41437-022-00577-3 · 2023 · External reference
Integrative genomics viewer
10.1038/nbt.1754 · 2011 · External reference
Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software
10.1038/nmeth.4458 · 2017 · External reference
ART: a next-generation sequencing read simulator
10.1093/bioinformatics/btr708 · 2012 · External reference
PBSIM3: a simulator for all types of PacBio and ONT long reads
2022 · External reference
Spatial-temporal targeted and non-targeted surveys to assess microbiological composition of drinking water in Puerto Rico following Hurricane Maria
2021 · External reference
The Sequence Read Archive: a decade more of explosive growth
10.1093/nar/gkab1053 · 2022 · External reference
GTDB-Tk v2: memory friendly classification with the Genome Taxonomy Database
10.1093/bioinformatics/btac672 · 2022 · External reference
CoverM: read alignment statistics for metagenomics
10.1093/bioinformatics/btaf147 · 2025 · External reference
Improved metagenome binning and assembly using deep variational autoencoders
10.1038/s41587-020-00777-4 · 2021 · External reference
A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments
10.1038/s41467-022-29843-y · 2022 · External reference
Analysis of metagenomic data
10.1038/s43586-024-00376-6 · 2025 · External reference
Shotgun metagenomics, from sampling to analysis
10.1038/nbt.3935 · 2017 · External reference
Critical Assessment of Metagenome Interpretation: the second round of challenges
10.1038/s41592-022-01431-4 · 2022 · External reference
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4
10.1038/s41587-023-01688-w · 2023 · External reference
Benchmarking metagenomic binning tools on real datasets across sequencing platforms and binning modes
10.1038/s41467-025-57957-6 · 2025 · External reference
Unveiling microbial diversity: harnessing long-read sequencing technology
10.1038/s41592-024-02262-1 · 2024 · External reference
Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing
10.1038/s41592-022-01539-7 · 2022 · External reference
Metagenomics-enabled microbial surveillance
10.1038/s41564-022-01089-w · 2022 · External reference
Clinical metagenomics for diagnosis and surveillance of viral pathogens
10.1038/s41579-025-01223-5 · 2026 · External reference
Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis
10.1038/s41564-026-02334-2 · 2026 · External reference
A global perspective on evolving bioinformatics and data science training needs
10.1093/bib/bbx100 · 2019 · External reference
Machine learning applications in genetics and genomics
10.1038/nrg3920 · 2015 · External reference
Deep learning for computational biology
10.15252/msb.20156651 · 2016 · External reference
Synthetic data in machine learning for medicine and healthcare
10.1038/s41551-021-00751-8 · 2021 · External reference
A guide to machine learning for biologists
10.1038/s41580-021-00407-0 · 2022 · External reference
Synthetic data in biomedicine via generative artificial intelligence
10.1038/s44222-024-00245-7 · 2024 · External reference
Codon language embeddings provide strong signals for use in protein engineering
10.1038/s42256-024-00791-0 · 2024 · External reference
Navigating the pitfalls of applying machine learning in genomics
10.1038/s41576-021-00434-9 · 2022 · External reference
metaSPAdes: a new versatile metagenomic assembler
10.1101/gr.213959.116 · 2017 · External reference
Unresolved reference
2014 · External reference
The Sequence Alignment/Map format and SAMtools
10.1093/bioinformatics/btp352 · 2009 · External reference
Minimap2: pairwise alignment for nucleotide sequences
10.1093/bioinformatics/bty191 · 2018 · External reference
BEDTools: a flexible suite of utilities for comparing genomic features
10.1093/bioinformatics/btq033 · 2010 · External reference
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
10.7717/peerj.7359 · 2019 · External reference
CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning
10.1038/s41592-023-01940-w · 2023 · External reference
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy
10.1093/nar/gkab776 · 2022 · External reference
Docker: lightweight Linux containers for consistent development and deployment
2014 · External reference
GenBank 2023 update
10.1093/nar/gkac1012 · 2023 · External reference
Collection and curation of prokaryotic genome assemblies from type strains at NCBI
10.1099/ijsem.0.005707 · 2023 · External reference
