Searching journal content for articles similar to Sun et al. 33 (4): 612.

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  1. Method: Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors
    • Mara Lohde,
    • Gabriel E. Wagner,
    • Johanna Dabernig-Heinz,
    • Adrian Viehweger,
    • Sascha D. Braun,
    • Stefan Monecke,
    • Celia Diezel,
    • Claudia Stein,
    • Mike Marquet,
    • Ralf Ehricht,
    • Mathias W. Pletz,
    • and Christian Brandt
    Genome Res. November 2024 34: 2039-2047; Published in Advance October 23, 2024, doi:10.1101/gr.278848.123
    ..., Schleenvoigt BT, Edel B, Pletz MW, Brandt C. 2022. A rare case of periprosthetic streptobacillosis - rapid identification via nanopore sequencing after inconclusive VITEK MS results. Arch Clin Med Case Rep 6: 613–617. doi:10.26502/acmcr.96550529 ↵Tourancheau A, Mead EA, Zhang X-S, Fang G. 2021. Discovering...
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  2. Review: Leveraging the power of long reads for targeted sequencing
    • Shruti V. Iyer,
    • Sara Goodwin,
    • and William Richard McCombie
    Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
    ...be noted that as of 2020, 10x Genomics has discontinued the sale of its Chromium Genome and Exome products. Since barcoded linked-reads are no longer available on this platform, it is not compatible with CATCH at present.Cas9-based targeted sequencing on the nanopore platformThe next wave of CRISPR...
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  3. Method: Analyzing rare mutations in metagenomes assembled using long and accurate reads
    • Marcus W. Fedarko,
    • Mikhail Kolmogorov,
    • and Pavel A. Pevzner
    Genome Res. November/December 2022 32: 2119-2133; Published in Advance November 23, 2022, doi:10.1101/gr.276917.122
    ...the FDR of identified rare mutations in a meta and further extend this idea by developing a context-dependent TDA.We show that deep HiFi-based sequencing can reveal tens of thousands of mutations (with controlled FDR) in a MAG and that these mutations can form hotspots (that may point to selection...
  4. Perspective: A vision for ubiquitous sequencing
    • Yaniv Erlich
    Genome Res. October 2015 25: 1411-1416; doi:10.1101/gr.191692.115
    ...solve certain engineering complications, such as access to fresh water and a place to drain sequencing waste (although access to electricity may be complicated). Most toilets are designed to have space below the water tank, which is rarely occupied. This could be a convenient area to place a small...
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  5. 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
    .... The fundamental tasks are to classify or group sequencing reads into distinct genomic bins, each representing a different taxon (e.g., species or strain) within a metagenomic sample (taxonomic binning), and to identify the taxa present while estimating their relative abundances in the sample (taxonomic profiling...
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  6. Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
    • Medhat Mahmoud,
    • Daniel P. Agustinho,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
    ...methods.Two leading long-read sequencing technologies currently dominate the market and have significantly impacted the genomics field (Fig. 1A): Pacific Biosciences (PacBio) HiFi and Oxford Nanopore Technologies (ONT) sequencing. While both technologies produce continuous long reads, they present...
  7. Method: Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors
    • Nitan Shalon,
    • David A. Relman,
    • and Eitan Yaffe
    Genome Res. May 2022 32: 986-1003; Published in Advance April 12, 2022, doi:10.1101/gr.275894.121
    ...in the biological sample. These phantom walks are a result of identical (or nearly identical) DNA sequences appearing in different genomic contexts. Repeat elements such as transposons and integrated phage are common in microbial s. Moreover, natural microbial communities have been shown to simultaneously harbor...
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  8. Review: Accurate and complete genomes from metagenomes
    • Lin-Xing Chen,
    • Karthik Anantharaman,
    • Alon Shaiber,
    • A. Murat Eren,
    • and Jillian F. Banfield
    Genome Res. March 2020 30: 315-333; Published in Advance March 18, 2020, doi:10.1101/gr.258640.119
    ...-quality draft sequences to complete s from metasGenome curation to completion is rarely undertaken (Table 1) because there is no single tool available to accomplish it, and there can be confusing complications. The procedure requires the steps described in the previous section as well as extension of scaffolds...
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  9. Research: The chromatin landscape of the histone-possessing Bacteriovorax bacteria
    • Georgi K. Marinov,
    • Benjamin Doughty,
    • Anshul Kundaje,
    • and William J. Greenleaf
    Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124
    ...have not been assayed so far with functional genomic tools in the bacterial clades that have histones.To begin addressing these outstanding issues, we have mapped chromatin accessibility using assay for transposase-accessible chromatin using sequencing (ATAC-seq) (Buenrostro et al. 2013...
  10. Method: metaSPAdes: a new versatile metagenomic assembler
    • Sergey Nurk,
    • Dmitry Meleshko,
    • Anton Korobeynikov,
    • and Pavel A. Pevzner
    Genome Res. May 2017 27: 824-834; Published in Advance March 15, 2017, doi:10.1101/gr.213959.116
    ...al. 2011. Enterotypes of the human gut microbiome. Nature 473: 1–7. Ashton PM, Nair S, Dallman T, Rubino S, Rabsch W, Mwaigwisya S, Wain J, O’Grady J. 2014. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat Biotechnol 33: 296...
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