Searching journal content for articles similar to Kim et al. 26 (12): 1721.

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  1. Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
    • Wenhai Zhang,
    • Yuansheng Liu,
    • Guangyi Li,
    • Jialu Xu,
    • Enlian Chen,
    • Alexander Schönhuth,
    • and Xiao Luo
    Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
    .... Consequently, understanding the diversity in terms of strains in microbial communities is crucial, as variations between strains can lead to different phenotypic expressions or diverse biological functions. However, current methods for taxonomic classification from metagenomic sequencing data have several...
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  2. Method: Real-time analysis and visualization of nanopore metagenomic samples with MARTi
    • Ned Peel,
    • Samuel Martin,
    • Darren Heavens,
    • Douglas W. Yu,
    • Matthew D. Clark,
    • and Richard M. Leggett
    Genome Res. November 2025 35: 2488-2500; Published in Advance October 27, 2025, doi:10.1101/gr.280550.125
    ...-source software tool that enables real-time analysis, visualization, and exploration of metagenomic sequencing data. MARTi allows users to choose a classification method (Kraken2, Centrifuge, BLAST [Camacho et al. 2009], or DIAMOND [Buchfink et al. 2021]), customize classification parameters, and provide...
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  3. Method: Robust 16S rRNA classification based on a compressed LCA index
    • Omar Ahmed,
    • Christina Boucher,
    • and Ben Langmead
    Genome Res. December 2025 35: 2650-2660; Published in Advance August 25, 2025, doi:10.1101/gr.279846.124
    ..., Gainesville, Florida 32611, USA Corresponding author: langmea@cs.jhu.eduAbstractTaxonomic sequence classification is a computational problem central to the study of metagenomics and evolution. Advances in compressed indexing with the r-index enable full-text pattern matching against large sequence collections...
  4. Method: Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters
    • Jens-Uwe Ulrich and
    • Bernhard Y. Renard
    Genome Res. June 2024 34: 914-924; Published in Advance June 17, 2024, doi:10.1101/gr.278623.123
    ...-sampling approach for metagenomic classification of short reads (Wood et al. 2019; Piro et al. 2020). However, Edgar (2021) recently showed that syncmers are more sensitive for selecting conserved k-mers in biological sequences, and Dutta et al. (2022) could also improve long-read mapping by using OCSs instead...
  5. Method: High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing
    • Nicholas D. Sanderson,
    • Jeremy Swann,
    • Leanne Barker,
    • James Kavanagh,
    • Sarah Hoosdally,
    • Derrick Crook,
    • The GonFast Investigators Group,
    • Teresa L. Street,
    • and David W. Eyre
    Genome Res. September 2020 30: 1354-1363; Published in Advance September 1, 2020, doi:10.1101/gr.262865.120
    ....24.8.1900118 ↵Kim D, Song L, Breitwieser FP, Salzberg SL. 2016. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res 26: 1721–1729. doi:10.1101/gr.210641.116 ↵Li H. 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34: 3094–3100. doi:10.1093/bioinformatics...
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  6. Method: taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable time
    • André Corvelo,
    • Wayne E. Clarke,
    • Nicolas Robine,
    • and Michael C. Zody
    Genome Res. May 2018 28: 751-758; Published in Advance March 27, 2018, doi:10.1101/gr.225276.117
    ..., Auch AF, Qi J, Schuster SC. 2007. MEGAN analysis of metagenomic data. Genome Res 17: 377–386. ↵Kim D, Song L, Breitwieser FP, Salzberg SL. 2016. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res 26: 1721–1729. ↵Leinonen R, Sugawara H, Shumway M, International...
  7. Resource: Windshield splatter analysis with the Galaxy metagenomic pipeline
    • Sergei Kosakovsky Pond,
    • Samir Wadhawan,
    • Francesca Chiaromonte,
    • Guruprasad Ananda,
    • Wen-Yu Chung,
    • James Taylor,
    • Anton Nekrutenko,
    • and The Galaxy Team
    Genome Res. November 2009 19: 2144-2153; Published in Advance October 9, 2009, doi:10.1101/gr.094508.109
    ...take advantage of any Galaxy tools to further process these data. Conclusion The explosive growth of metagenomics in the past 2–3 yr can be mainly attributed to the rapid proliferation of massively parallel sequencing technologies. This trend is almost certain to continue, and as a result, the future...
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  8. Method: Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm
    • Samuel T. Horsfield,
    • Basil C.T. Fok,
    • Yuhan Fu,
    • Paul Turner,
    • John A. Lees,
    • and Nicholas J. Croucher
    Genome Res. April 2025 35: 1025-1040; Published in Advance March 4, 2025, doi:10.1101/gr.279435.124
    ..., ejecting the fragment (Payne et al. 2021). NAS increases target sequence yield by rejecting nontarget DNA, increasing the sensitivity for detecting of sequences of interest (Payne et al. 2021; Weilguny et al. 2023). This makes NAS well-suited for metagenomics, the culture-free DNA sequencing-based analysis...
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  9. Method: Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
    • Yuhong Sun,
    • Zhanwen Cheng,
    • Xiang Li,
    • Qing Yang,
    • Bixi Zhao,
    • Ziqi Wu,
    • and Yu Xia
    Genome Res. April 2023 33: 612-621; Published in Advance April 11, 2023, doi:10.1101/gr.277266.122
    ..., Salzberg SL. 2016. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res 26: 1721–1729. doi:10.1101/gr.210641.116 ↵Kipp EJ, Lindsey LL, Milstein MS, Blanco CM, Baker JP, Faulk C, Oliver JD, Larsen PA. 2023. Nanopore adaptive sampling for targeted mitochondrial sequencing...
  10. Method: Efficient taxa identification using a pangenome index
    • Omar Ahmed,
    • Massimiliano Rossi,
    • Christina Boucher,
    • and Ben Langmead
    Genome Res. July 2023 33: 1069-1077; Published in Advance May 31, 2023, doi:10.1101/gr.277642.123
    ...prokaryotic s reveals clear species boundaries. Nat Commun 9: 5114. doi:10.1038/s41467-018-07641-9 ↵Kim D, Song L, Breitwieser FP, Salzberg SL. 2016. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res 26: 1721–1729. doi:10.1101/gr.210641.116 ↵Kovaka S, Fan Y, Ni B, Timp W...
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