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CAMISIM: Simulating metagenomes and microbial communities

https://doi.org/10.1101/300970
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What this work says

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

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Metagenomics and CAZyme Discovery
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Multidimensional Scaling by Optimizing Goodness of Fit to a Nonmetric Hypothesis
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Distinct Microbial Communities Trigger Colitis Development upon Intestinal Barrier Damage via Innate or Adaptive Immune Cells
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The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease
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Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
inferredcites →https://doi.org/10.1038/ismej.2015.249openalex-snapshot
High-resolution phylogenetic microbial community profiling
inferredcites →https://doi.org/10.1038/nature06244openalex-snapshot
The Human Microbiome Project
inferredcites →https://doi.org/10.1038/nature06269openalex-snapshot
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
inferredcites →https://doi.org/10.1038/nature11234openalex-snapshot
Structure, function and diversity of the healthy human microbiome
inferredcites →https://doi.org/10.1038/nature12352openalex-snapshot
Insights into the phylogeny and coding potential of microbial dark matter
inferredcites →https://doi.org/10.1038/nature24621openalex-snapshot
A communal catalogue reveals Earth’s multiscale microbial diversity
inferredcites →https://doi.org/10.1038/nbt.2579openalex-snapshot
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
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.2939openalex-snapshot
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
inferredcites →https://doi.org/10.1038/nbt.3329openalex-snapshot
Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning
inferredcites →https://doi.org/10.1038/nbt.3353openalex-snapshot
A catalog of the mouse gut metagenome
inferredcites →https://doi.org/10.1038/nbt.3935openalex-snapshot
Shotgun metagenomics, from sampling to analysis
inferredcites →https://doi.org/10.1038/nmeth.3103openalex-snapshot
Binning metagenomic contigs by coverage and composition
inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot
Fast and sensitive protein alignment using DIAMOND
inferredcites →https://doi.org/10.1038/nmeth.3802openalex-snapshot
Strain-level microbial epidemiology and population genomics from shotgun metagenomics
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/nrg.2016.49openalex-snapshot
Coming of age: ten years of next-generation sequencing technologies
inferredcites →https://doi.org/10.1038/s41467-017-01086-2openalex-snapshot
Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics
inferredcites →https://doi.org/10.1038/sdata.2016.81openalex-snapshot
Next generation sequencing data of a defined microbial mock community
inferredcites →https://doi.org/10.1073/pnas.0409727102openalex-snapshot
Genomic insights that advance the species definition for prokaryotes
inferredcites →https://doi.org/10.1073/pnas.1000604107openalex-snapshot
Combined niche and neutral effects in a microbial wastewater treatment community
inferredcites →https://doi.org/10.1093/bib/bbv029openalex-snapshot
Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction
inferredcites →https://doi.org/10.1093/bioinformatics/btl529openalex-snapshot
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btr708openalex-snapshot
ART: a next-generation sequencing read simulator
inferredcites →https://doi.org/10.1093/bioinformatics/bts174openalex-snapshot
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
inferredcites →https://doi.org/10.1093/bioinformatics/bts649openalex-snapshot
PBSIM: PacBio reads simulator—toward accurate genome assembly
inferredcites →https://doi.org/10.1093/bioinformatics/btt086openalex-snapshot
QUAST: quality assessment tool for genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btv033openalex-snapshot
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
inferredcites →https://doi.org/10.1093/bioinformatics/btv383openalex-snapshot
Bandage: interactive visualization of de novo genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btw144openalex-snapshot
MeCorS: Metagenome-enabled error correction of single cell sequencing reads
inferredcites →https://doi.org/10.1093/gigascience/gix010openalex-snapshot
NanoSim: nanopore sequence read simulator based on statistical characterization
inferredcites →https://doi.org/10.1093/nar/gkl842openalex-snapshot
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
inferredcites →https://doi.org/10.1093/nar/gks251openalex-snapshot
Grinder: a versatile amplicon and shotgun sequence simulator
inferredcites →https://doi.org/10.1093/nar/gkv1070openalex-snapshot
KEGG as a reference resource for gene and protein annotation
inferredcites →https://doi.org/10.1093/nar/gkv657openalex-snapshot
Microbial species delineation using whole genome sequences
inferredcites →https://doi.org/10.1101/155358openalex-snapshot
Evaluating Metagenome Assembly on a Simple Defined Community with Many Strain Variants
inferredcites →https://doi.org/10.1101/gr.213959.116openalex-snapshot
metaSPAdes: a new versatile metagenomic assembler
inferredcites →https://doi.org/10.1101/gr.2289704openalex-snapshot
Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements
inferredcites →https://doi.org/10.1111/j.1365-294x.2010.04948.xopenalex-snapshot
Species abundance distributions and richness estimations in fungal metagenomics - lessons learned from community ecology
inferredcites →https://doi.org/10.1111/j.1600-0706.2009.18236.xopenalex-snapshot
A meta‐analysis of species–abundance distributions
inferredcites →https://doi.org/10.1126/science.1200387openalex-snapshot
Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen
inferredcites →https://doi.org/10.1126/science.1261359openalex-snapshot
Structure and function of the global ocean microbiome
inferredcites →https://doi.org/10.1186/1471-2105-15-s9-s14openalex-snapshot
A better sequence-read simulator program for metagenomics
inferredcites →https://doi.org/10.1186/1756-0500-7-533openalex-snapshot
FASTQSim: platform-independent data characterization and in silico read generation for NGS datasets
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/s13059-017-1309-9openalex-snapshot
DESMAN: a new tool for de novo extraction of strains from metagenomes
inferredcites →https://doi.org/10.1186/s13068-016-0565-3openalex-snapshot
Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants
inferredcites →https://doi.org/10.1186/s13742-015-0073-6openalex-snapshot
Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant
inferredcites →https://doi.org/10.1186/s13742-015-0087-0openalex-snapshot
Bioboxes: standardised containers for interchangeable bioinformatics software
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.0031386openalex-snapshot
Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
inferredcites →https://doi.org/10.1371/journal.pone.0075448openalex-snapshot
NeSSM: A Next-Generation Sequencing Simulator for Metagenomics
inferredcites →https://doi.org/10.7717/peerj.1165openalex-snapshot
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
inferredcites →https://doi.org/10.7717/peerj.2676openalex-snapshot
Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C)
inferredcites →https://doi.org/10.7717/peerj.603openalex-snapshot
GroopM: an automated tool for the recovery of population genomes from related metagenomes

What points at this work

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

inferred← citeshttps://doi.org/10.1016/j.csbj.2020.11.049openalex-snapshot
Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods
inferred← citeshttps://doi.org/10.1038/s41467-022-28581-5openalex-snapshot
Genome binning of viral entities from bulk metagenomics data
inferred← citeshttps://doi.org/10.1038/s41467-024-46539-7openalex-snapshot
BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis
inferred← citeshttps://doi.org/10.1038/s41467-024-52907-0openalex-snapshot
HyLight: Strain aware assembly of low coverage metagenomes
inferred← citeshttps://doi.org/10.1038/s41564-023-01484-xopenalex-snapshot
Challenges and opportunities in sharing microbiome data and analyses
inferred← citeshttps://doi.org/10.1038/s41587-023-01799-4openalex-snapshot
Phage-inclusive profiling of human gut microbiomes with Phanta
inferred← citeshttps://doi.org/10.1038/s41592-022-01431-4openalex-snapshot
Critical Assessment of Metagenome Interpretation: the second round of challenges
inferred← citeshttps://doi.org/10.1038/s41596-020-00480-3openalex-snapshot
Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit
inferred← citeshttps://doi.org/10.1093/bioinformatics/btae760openalex-snapshot
MeSS and assembly_finder: a toolkit for in silico metagenomic sample generation
inferred← citeshttps://doi.org/10.1093/gigascience/giad013openalex-snapshot
Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim
inferred← citeshttps://doi.org/10.1093/gigascience/giy069openalex-snapshot
AMBER: Assessment of Metagenome BinnERs
inferred← citeshttps://doi.org/10.1093/gigascience/giz154openalex-snapshot
CAMITAX: Taxon labels for microbial genomes
inferred← citeshttps://doi.org/10.1101/2024.05.09.593079openalex-snapshot
Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat
inferred← citeshttps://doi.org/10.1101/372680openalex-snapshot
Assessing taxonomic metagenome profilers with OPAL
inferred← citeshttps://doi.org/10.11606/t.95.2022.tde-19072022-153242openalex-snapshot
Recovery of high-quality MAGs in time-serial metagenomic data and FixAME development: an assisting curation tool of genomic assembly error
inferred← citeshttps://doi.org/10.1186/s13059-019-1646-yopenalex-snapshot
Assessing taxonomic metagenome profilers with OPAL
inferred← citeshttps://doi.org/10.1186/s13059-023-03040-6openalex-snapshot
happi: a hierarchical approach to pangenomics inference
inferred← citeshttps://doi.org/10.1186/s40168-019-0626-5openalex-snapshot
Choice of assembly software has a critical impact on virome characterisation
inferred← citeshttps://doi.org/10.21203/rs.3.rs-1125389/v1openalex-snapshot
Characterization and Simulation of Metagenomic Nanopore Sequencing Data with Meta-NanoSim
inferred← citeshttps://doi.org/10.21203/rs.3.rs-131495/v1openalex-snapshot
Exploring Quantitative Metagenomics Studies using Oxford Nanopore Sequencing: A Computational and Experimental Protocol
inferred← citeshttps://doi.org/10.21203/rs.3.rs-287089/v1openalex-snapshot
Simulation Study and Comparative Evaluation of Viral Contiguous Sequence Identification Tools
inferred← citeshttps://doi.org/10.21203/rs.3.rs-3433959/v1openalex-snapshot
Impact of simulation and reference catalogues on the evaluation of taxonomic profiling pipelines
inferred← citeshttps://doi.org/10.21203/rs.3.rs-3433959/v2openalex-snapshot
Impact of simulation and reference catalogues on the evaluation of taxonomic profiling pipelines
inferred← citeshttps://doi.org/10.3390/genes12101496openalex-snapshot
Exploring Semi-Quantitative Metagenomic Studies Using Oxford Nanopore Sequencing: A Computational and Experimental Protocol
inferred← citeshttps://doi.org/10.5204/thesis.eprints.248733openalex-snapshot
Bioinformatic tool development and application to the human gut microbiome
inferred← citeshttps://doi.org/10.70675/bc11fdd1z0c3az45c3z9f9ez65301994b39dopenalex-snapshot
Continuous embeddings for large-scale machine learning with DNA sequences
inferred← citeshttps://doi.org/10.7287/peerj.10119v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Biases in genome reconstruction from metagenomic data (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.10119v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Biases in genome reconstruction from metagenomic data (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.10119v0.1/reviews/3openalex-snapshot
Peer Review #3 of "Biases in genome reconstruction from metagenomic data (v0.1)"
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