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References from Perseus: lineage-aware refinement of Kraken2 taxonomic classification for long read metagenomes. Local targets link to admitted publications; unresolved targets remain external evidence.
Unveiling microbial diversity: harnessing long-read sequencing technology
10.1038/s41592-024-02262-1 · 2024 · External reference
Enumerating soil biodiversity
10.1073/pnas.2304663120 · 2023 · External reference
Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes
10.1093/gigascience/giaf135 · 2025 · External reference
Unearthing soil biodiversity through collaborative genomic research and education
10.1038/s41588-025-02442-5 · 2026 · External reference
Managing false positives during detection of pathogen sequences in shotgun metagenomics datasets
10.1186/s12859-024-05952-x · 2024 · External reference
KrakenUniq: confident and fast metagenomics classification using unique k-mer counts
10.1186/s13059-018-1568-0 · 2018 · External reference
MeSS and assembly_finder: a toolkit for in silico metagenomic sample generation
10.1093/bioinformatics/btae760 · 2024 · External reference
Accessing the soil metagenome for studies of microbial diversity
10.1128/aem.01526-10 · 2011 · External reference
An in-depth evaluation of metagenomic classifiers for soil microbiomes
10.1186/s40793-024-00561-w · 2024 · External reference
Drastic reduction of false positive species in samples of insects by intersecting the default output of two popular metagenomic classifiers
10.1371/journal.pone.0275790 · 2022 · External reference
Metabuli: sensitive and specific metagenomic classification via joint analysis of amino acid and DNA
10.1038/s41592-024-02273-y · 2024 · External reference
Minimap2: pairwise alignment for nucleotide sequences
10.1093/bioinformatics/bty191 · 2018 · External reference
Impact of database choice and confidence score on the performance of taxonomic classification using Kraken2
10.1007/s42994-024-00178-0 · 2024 · External reference
Metagenome analysis using the Kraken software suite
10.1038/s41596-022-00738-y · 2022 · External reference
MUMmer4: a fast and versatile genome alignment system
10.1371/journal.pcbi.1005944 · 2018 · External reference
Comparative analysis of metagenomic classifiers for long-read sequencing datasets
10.1186/s12859-024-05634-8 · 2024 · External reference
Comprehensive benchmarking and ensemble approaches for metagenomic classifiers
10.1186/s13059-017-1299-7 · 2017 · External reference
Critical assessment of metagenome interpretation: the second round of challenges
10.1038/s41592-022-01431-4 · 2022 · External reference
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification
10.1186/s13059-018-1554-6 · 2018 · External reference
Refining filtering criteria of Kraken family of tools for accurate taxonomic profiling of ancient metagenomic data
10.3389/fmicb.2026.1603339 · 2026 · External reference
Investigation of machine learning algorithms for taxonomic classification of marine metagenomes
10.1128/spectrum.05237-22 · 2023 · External reference
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes
10.1093/nar/gkaf1040 · 2025 · External reference
Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets
10.1186/s12859-022-05103-0 · 2022 · External reference
BEDTools: a flexible suite of utilities for comparing genomic features
10.1093/bioinformatics/btq033 · 2010 · External reference
Insights into the phylogeny and coding potential of microbial dark matter
10.1038/nature12352 · 2013 · External reference
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification: find out more about bakta, the motivation, challenges and applications, here
10.1099/mgen.0.000685 · 2021 · External reference
Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats
10.1038/s41564-025-02062-z · 2025 · External reference
Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification
10.1186/s13059-024-03244-4 · 2024 · External reference
10.1101/2023.10.20.563221
10.1101/2023.10.20.563221 · 2023 · External reference
10.1101/2025.06.18.660363
10.1101/2025.06.18.660363 · 2025 · External reference
Removal of false positives in metagenomics-based taxonomy profiling via targeting type iib restriction sites
10.1038/s41467-023-41099-8 · 2023 · External reference
Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved xor filters
10.1101/gr.278623.123 · 2024 · External reference
Improved metagenomic analysis with Kraken 2
10.1186/s13059-019-1891-0 · 2019 · External reference
Long-read metagenomics improves the recovery of viral diversity from complex natural marine samples
10.1128/msystems.00192-22 · 2022 · External reference