Research graph
References from Benchmarking of Reference‐Based Tools for Strain‐Level Resolution of Plant Microbiome. Local targets link to admitted publications; unresolved targets remain external evidence.
Plant Beneficial Endophytic Bacteria: Mechanisms, Diversity, Host Range and Genetic Determinants
10.1016/j.micres.2019.02.001 · 2019 · External reference
Strain Profiling and Epidemiology of Bacterial Species From Metagenomic Sequencing
10.1038/s41467-017-02209-5 · 2017 · External reference
Unresolved reference
External reference
Computational Methods for Strain‐Level Microbial Detection in Colony and Metagenome Sequencing Data
10.3389/fmicb.2020.01925 · 2020 · External reference
Metagenome Assembly and Annotation of Data From the Rhizosphere Soil of Drought‐Stressed CRN‐3505 Maize Cultivar
10.1016/j.dib.2024.110966 · 2024 · External reference
Functional Overlap of the Arabidopsis Leaf and Root Microbiota
10.1038/nature16192 · 2015 · External reference
Summarizing and Correcting the GC Content Bias in High‐Throughput Sequencing
10.1093/nar/gks001 · 2012 · External reference
Extending and Improving Metagenomic Taxonomic Profiling With Uncharacterized Species Using MetaPhlAn 4
10.1038/s41587-023-01688-w · 2023 · External reference
KrakenUniq: Confident and Fast Metagenomics Classification Using Unique k‐Mer Counts
10.1186/s13059-018-1568-0 · 2018 · External reference
Soil Origin and Plant Genotype Structure Distinct Microbiome Compartments in the Model Legume Medicago truncatula
10.1186/s40168-020-00915-9 · 2020 · External reference
fastp: an ultra‐fast all‐in‐one FASTQ preprocessor
10.1093/bioinformatics/bty560 · 2018 · External reference
Twelve Years of SAMtools and BCFtools
10.1093/gigascience/giab008 · 2021 · External reference
NanoPack: Visualizing and Processing Long‐Read Sequencing Data
10.1093/bioinformatics/bty149 · 2018 · External reference
Structure, Variation and Assembly of the Root‐Associated Microbiomes of Rice
10.1073/pnas.1414592112 · 2015 · External reference
Key Challenges in Plant Microbiome Research in the Next Decade
10.3390/microorganisms13112546 · 2025 · External reference
Simulating Illumina Metagenomic Data With InSilicoSeq
10.1093/bioinformatics/bty630 · 2019 · External reference
Are We Throwing Away Good Data? Evaluation of Chimera Detection Algorithms on Long‐Read Amplicons Reveals High False‐Positive Rates Across Algorithms
10.7717/peerj.20456 · 2025 · External reference
Characterizing Rhizosphere Microbiota of Peanut ( Arachis hypogaea L.) From Pre‐Sowing to Post‐Harvest of Crop Under Field Conditions
10.1038/s41598-021-97071-3 · 2021 · External reference
A Review on Evaluation Metrics for Data Classification Evaluations
2015 · External reference
High Throughput ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Boundaries
10.1038/s41467-018-07641-9 · 2018 · External reference
Fast Gapped‐Read Alignment With Bowtie 2
10.1038/nmeth.1923 · 2012 · External reference
Metalign: Efficient Alignment‐Based Metagenomic Profiling via Containment Min Hash
10.1186/s13059-020-02159-0 · 2020 · External reference
Minimap2: Pairwise Alignment for Nucleotide Sequences
10.1093/bioinformatics/bty191 · 2018 · External reference
High‐Resolution Strain‐Level Microbiome Composition Analysis From Short Reads
10.1186/s40168-023-01615-w · 2023 · External reference
The Soil‐Plant‐Human Gut Microbiome Axis Into Perspective
10.1038/s41467-025-62989-z · 2025 · External reference
Systematic Benchmarking of Omics Computational Tools
10.1038/s41467-019-09406-4 · 2019 · External reference
Comprehensive Benchmarking and Ensemble Approaches for Metagenomic Classifiers
10.1186/s13059-017-1299-7 · 2017 · External reference
Strain‐Level Identification of Bacterial Tomato Pathogens Directly From Metagenomic Sequences
10.1094/phyto-09-19-0351-r · 2020 · External reference
Environmental and Human Microbiome for Health
10.3390/life12030456 · 2022 · External reference
Deciphering the Role of Rhizosphere Microbiota in Modulating Disease Resistance in Cabbage Varieties
10.1186/s40168-024-01883-0 · 2024 · External reference
Frequency‐Based Haplotype Reconstruction From Deep Sequencing Data of Bacterial Populations
10.1093/nar/gkv478 · 2015 · External reference
DESMAN: A New Tool for de Novo Extraction of Strains From Metagenomes
10.1186/s13059-017-1309-9 · 2017 · External reference
Rhizosphere Shotgun Metagenomic Analyses Fail to Show Differences Between Ancestral and Modern Wheat Genotypes Grown Under Low Fertilizer Inputs
10.1093/femsec/fiab071 · 2021 · External reference
From Squiggle to Basepair: Computational Approaches for Improving Nanopore Sequencing Read Accuracy
10.1186/s13059-018-1462-9 · 2018 · External reference
Metagenomic Sequencing for Identification of Xylella fastidiosa From Leaf Samples
10.1128/msystems.00591-21 · 2021 · External reference
10.1111/pce.15429
10.1111/pce.15429 · External reference
Introducing Mothur: Open‐Source, Platform‐Independent, Community‐Supported Software for Describing and Comparing Microbial Communities
10.1128/aem.01541-09 · 2009 · External reference
Benchmarking Metagenomics Tools for Taxonomic Classification
10.1016/j.cell.2019.07.010 · 2019 · External reference
The Landscape of Genetic Content in the Gut and Oral Human Microbiome
10.1016/j.chom.2019.07.008 · 2019 · External reference
Plant–Microbiome Interactions: From Community Assembly to Plant Health
10.1038/s41579-020-0412-1 · 2020 · External reference
The Plant Microbiome
10.1186/gb-2013-14-6-209 · 2013 · External reference
StrainGE: A Toolkit to Track and Characterize Low‐Abundance Strains in Complex Microbial Communities
10.1186/s13059-022-02630-0 · 2022 · External reference
Diversity Within Species: Interpreting Strains in Microbiomes
10.1038/s41579-020-0368-1 · 2020 · External reference
PStrain: An Iterative Microbial Strains Profiling Algorithm for Shotgun Metagenomic Sequencing Data
10.1093/bioinformatics/btaa1056 · 2020 · External reference
MIDAS2: Metagenomic Intra‐Species Diversity Analysis System
10.1093/bioinformatics/btac713 · 2023 · External reference
