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Evaluating Metagenome Assembly on a Simple Defined Community with Many Strain Variants

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What this work says

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

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Prevalence and distribution of intervertebral disc degeneration over the entire spine in a population-based cohort: the Wakayama Spine Study

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MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

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Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

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Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision

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/nmeth.4458openalex-snapshot

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

inferredcites →https://doi.org/10.1038/nmeth1043openalex-snapshot

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

inferredcites →https://doi.org/10.1073/pnas.1402564111openalex-snapshot

Tackling soil diversity with the assembly of large, complex metagenomes

inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

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/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/gigascience/gix007openalex-snapshot

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach

inferredcites →https://doi.org/10.1093/nar/gkx348openalex-snapshot

BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation

inferredcites →https://doi.org/10.1101/150722openalex-snapshot

Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C

inferredcites →https://doi.org/10.1101/gr.089532.108openalex-snapshot

ABySS: A parallel assembler for short read sequence data

inferredcites →https://doi.org/10.1101/gr.142315.112openalex-snapshot

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

inferredcites →https://doi.org/10.1101/gr.183012.114openalex-snapshot

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

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

metaSPAdes: a new versatile metagenomic assembler

inferredcites →https://doi.org/10.1101/gr.214155.116openalex-snapshot

Genome graphs and the evolution of genome inference

inferredcites →https://doi.org/10.1101/gr.5894107openalex-snapshot

Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi

inferredcites →https://doi.org/10.1101/gr.828403openalex-snapshot

Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2

inferredcites →https://doi.org/10.1111/1462-2920.12086openalex-snapshot

Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities

inferredcites →https://doi.org/10.1111/1755-0998.12463openalex-snapshot

Potential and pitfalls of eukaryotic metagenome skimming: a test case for lichens

inferredcites →https://doi.org/10.1126/science.1072104openalex-snapshot

Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes

inferredcites →https://doi.org/10.1126/science.1162986openalex-snapshot

Real-Time DNA Sequencing from Single Polymerase Molecules

inferredcites →https://doi.org/10.1128/mbio.01669-15openalex-snapshot

Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs

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/10.1128/msystems.00045-16openalex-snapshot

Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes

inferredcites →https://doi.org/10.1186/1471-2164-12-1openalex-snapshot

Venom gland transcriptomes of two elapid snakes (Bungarus multicinctus and Naja atra) and evolution of toxin genes

inferredcites →https://doi.org/10.1186/1471-2164-12-s2-s8openalex-snapshot

Evaluation of short read metagenomic assembly

inferredcites →https://doi.org/10.1186/1471-2164-15-349openalex-snapshot

A network-based approach to identify substrate classes of bacterial glycosyltransferases

inferredcites →https://doi.org/10.1186/1471-2164-15-37openalex-snapshot

Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut

inferredcites →https://doi.org/10.1186/gb-2004-5-2-r12openalex-snapshot

Versatile and open software for comparing large genomes

inferredcites →https://doi.org/10.1186/s12864-017-3679-5openalex-snapshot

Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies

inferredcites →https://doi.org/10.1186/s12864-017-3918-9openalex-snapshot

Assembling metagenomes, one community at a time

inferredcites →https://doi.org/10.1186/s12915-014-0087-zopenalex-snapshot

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

inferredcites →https://doi.org/10.1186/s13059-016-0997-xopenalex-snapshot

Mash: fast genome and metagenome distance estimation using MinHash

inferredcites →https://doi.org/10.1186/s13073-020-00747-0openalex-snapshot

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale

inferredcites →https://doi.org/10.12688/f1000research.6924.1openalex-snapshot

The khmer software package: enabling efficient nucleotide sequence analysis

inferredcites →https://doi.org/10.1371/journal.pbio.1001920openalex-snapshot

Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains

inferredcites →https://doi.org/10.1371/journal.pone.0169662openalex-snapshot

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!

inferredcites →https://doi.org/10.1534/g3.114.011825openalex-snapshot

Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps

inferredcites →https://doi.org/10.21105/joss.00027openalex-snapshot

sourmash: a library for MinHash sketching of DNA

inferredcites →https://doi.org/10.3389/fgene.2014.00013openalex-snapshot

On the optimal trimming of high-throughput mRNA sequence data

inferredcites →https://doi.org/10.3389/fmicb.2015.01451openalex-snapshot

gbtools: Interactive Visualization of Metagenome Bins in R

inferredcites →https://doi.org/10.7287/peerj.preprints.890openalex-snapshot

Crossing the streams: a framework for streaming analysis of short DNA sequencing reads

inferredcites →https://doi.org/10.7287/peerj.preprints.890v1openalex-snapshot

Crossing the streams: a framework for streaming analysis of short DNA sequencing reads

inferredcites →https://doi.org/10.7554/elife.03318openalex-snapshot

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

inferredcites →https://doi.org/10.7717/peerj.415openalex-snapshot

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

What points at this work

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

inferred← citeshttps://doi.org/10.1007/978-1-4939-8728-3_12openalex-snapshot

Metagenome Assembly and Contig Assignment

inferred← citeshttps://doi.org/10.1016/j.syapm.2018.08.009openalex-snapshot

Relevance of phenotypic information for the taxonomy of not-yet-cultured microorganisms

inferred← citeshttps://doi.org/10.1093/gigascience/giaa125openalex-snapshot

Localized effect of treated wastewater effluent on the resistome of an urban watershed

inferred← citeshttps://doi.org/10.1093/gigascience/giy057openalex-snapshot

ASaiM: a Galaxy-based framework to analyze microbiota data

inferred← citeshttps://doi.org/10.1093/nar/gkac689openalex-snapshot

Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments

inferred← citeshttps://doi.org/10.1101/176644openalex-snapshot

Dynamic marine viral infections and major contribution to photosynthetic processes shown by regional and seasonal picoplankton metatranscriptomes

inferred← citeshttps://doi.org/10.1101/2022.01.11.475838openalex-snapshot

Lightweight compositional analysis of metagenomes with FracMinHash and minimum metagenome covers

inferred← citeshttps://doi.org/10.1101/2022.11.02.514947openalex-snapshot

Sourmash Branchwater Enables Lightweight Petabyte-Scale Sequence Search

inferred← citeshttps://doi.org/10.1101/300970openalex-snapshot

CAMISIM: Simulating metagenomes and microbial communities

inferred← citeshttps://doi.org/10.1101/367755openalex-snapshot

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language

inferred← citeshttps://doi.org/10.1111/2041-210x.14149openalex-snapshot

Reconstruction of small subunit ribosomal RNA from high‐throughput sequencing data: A comparative study of metagenomics and total RNA sequencing

inferred← citeshttps://doi.org/10.1128/spectrum.01434-21openalex-snapshot

Evaluating de Novo Assembly and Binning Strategies for Time Series Drinking Water Metagenomes

inferred← citeshttps://doi.org/10.1186/s12859-020-03590-7openalex-snapshot

SPAligner: alignment of long diverged molecular sequences to assembly graphs

inferred← citeshttps://doi.org/10.1186/s12885-025-14787-5openalex-snapshot

Highly-accurate prediction of colorectal cancer through low abundance uncultivated genomes recovered using metagenomic co-assembly and binning approach

inferred← citeshttps://doi.org/10.1186/s13059-019-1760-xopenalex-snapshot

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

inferred← citeshttps://doi.org/10.1186/s13059-019-1841-xopenalex-snapshot

Mash Screen: high-throughput sequence containment estimation for genome discovery

inferred← citeshttps://doi.org/10.1186/s13059-020-02066-4openalex-snapshot

Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity

inferred← citeshttps://doi.org/10.1186/s40168-018-0562-9openalex-snapshot

Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches

inferred← citeshttps://doi.org/10.1186/s40168-019-0633-6openalex-snapshot

CAMISIM: simulating metagenomes and microbial communities

inferred← citeshttps://doi.org/10.1186/s40168-019-0684-8openalex-snapshot

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language

inferred← citeshttps://doi.org/10.12688/f1000research.19675.1openalex-snapshot

Large-scale sequence comparisons with sourmash

inferred← citeshttps://doi.org/10.3389/fgene.2019.00957openalex-snapshot

Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes

inferred← citeshttps://doi.org/10.70675/c59f263czbd9fz43edz88d4z1eac5825e1faopenalex-snapshot

Développement et applications d'outils d'analyse métagénomique des communautés microbiennes associées aux insectes

inferred← citeshttps://doi.org/10.70675/d91a3321z646fz4691zb1f5z1e5039b15385openalex-snapshot

Modélisation de séquences et reconstruction non supervisée de génomes microbiens à partir de donnée métagénomiques.

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