Searching journal content for articles similar to Dolle et al. 27 (2): 300.

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  1. Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
    • Carolina Monzó,
    • Adam Frankish,
    • and Ana Conesa
    Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
    .... doi:10.1016/j.xgen.2024.100527 ↵de la Rubia I, Srivastava A, Xue W, Indi JA, Carbonell-Sala S, Lagarde J, Albà MM, Eyras E. 2022. RATTLE: reference-free reconstruction and quantification of transcriptomes from nanopore sequencing. Genome Biol 23: 153. doi:10.1186/s13059-022-02715-w ↵Dong X, Chen R...
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  2. Method: Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns
    • Alla Mikheenko,
    • Andrey D. Prjibelski,
    • Anoushka Joglekar,
    • and Hagen U. Tilgner
    Genome Res. April 2022 32: 726-737; Published in Advance March 17, 2022, doi:10.1101/gr.276405.121
    ...considering reads with detected barcodes. It is likely that allowing for barcode mismatches could lead to more ONT reads being retained, although that comes at the risk of introducing more inaccurate barcodes.Sequence comparison using reference-based and reference-free alignmentsOur downstream analysis mostly...
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  3. Review: Data structures based on k-mers for querying large collections of sequencing data sets
    • Camille Marchet,
    • Christina Boucher,
    • Simon J. Puglisi,
    • Paul Medvedev,
    • Mikaël Salson,
    • and Rayan Chikhi
    Genome Res. January 2021 31: 1-12; Published in Advance December 16, 2020, doi:10.1101/gr.260604.119
    ...or underway, including GEUVADIS (Lappalainen et al. 2013), GenomeTrakr (Timme et al. 2018), and MetaSUB (The MetaSUB International Consortium 2016). An overwhelming amount of public data is now available at EBI's European Nucleotide Archive (ENA) (Cook et al. 2019) and NCBI's Sequence Read Archive (SRA...
  4. Review: k-mer approaches for biodiversity genomics
    • Katharine M. Jenike,
    • Lucía Campos-Domínguez,
    • Marilou Boddé,
    • José Cerca,
    • Christina N. Hodson,
    • Michael C. Schatz,
    • and Kamil S. Jaron
    Genome Res. February 2025 35: 219-230; Published in Advance January 31, 2025, doi:10.1101/gr.279452.124
    ...reads analyzed with 21-mers, a sequencing error will disrupt 21 of the 80 k-mers in the read, except if the error is near the end of the read). The remaining k-mers will represent true genomic sequence.The second benefit is purely computational: Usually we analyze the k-mers that are the faithful...
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  5. Method: Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
    • Romain Derelle,
    • Johanna von Wachsmann,
    • Tommi Mäklin,
    • Joel Hellewell,
    • Timothy Russell,
    • Ajit Lalvani,
    • Leonid Chindelevitch,
    • Nicholas J. Croucher,
    • Simon R. Harris,
    • and John A. Lees
    Genome Res. October 2024 34: 1661-1673; Published in Advance October 15, 2024, doi:10.1101/gr.279449.124
    ...sequences that are aligned and on the same strand for clarity, but in real input data, neither is necessary. Split k-mers are used as keys, and their middle bases are stored in lists. This dictionary is compressed using snappy to make split k-mer files (SKFs). ska align makes reference-free alignments...
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  6. Method: Accurate and fast graph-based pangenome annotation and clustering with ggCaller
    • Samuel T. Horsfield,
    • Gerry Tonkin-Hill,
    • Nicholas J. Croucher,
    • and John A. Lees
    Genome Res. September 2023 33: 1622-1637; Published in Advance August 24, 2023, doi:10.1101/gr.277733.123
    ...clustering structurally diverse proteins.ggCaller improves functional interpretation in pan-wide association studiesggCaller supports querying of sequences of arbitrary length within an annotated DBG, enabling reference-free functional interpretation of sequence elements. This is useful when analyzing...
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  7. Method: Detection of simple and complex de novo mutations with multiple reference sequences
    • Kiran V. Garimella,
    • Zamin Iqbal,
    • Michael A. Krause,
    • Susana Campino,
    • Mihir Kekre,
    • Eleanor Drury,
    • Dominic Kwiatkowski,
    • Juliana M. Sá,
    • Thomas E. Wellems,
    • and Gil McVean
    Genome Res. August 2020 30: 1154-1169; Published in Advance August 19, 2020, doi:10.1101/gr.255505.119
    ...precludes the straightforward application of existing tools (Alkan et al. 2011; Tattini et al. 2015). A typical assembly graph stores genomic subsequences k-mers as vertices and sequence overlaps (read-to-read alignments or k − 1 substring matches) as edges (Flicek and Birney 2009). Repeats longer than...
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  8. Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
    • Alejandro Ceron-Noriega,
    • Miguel V. Almeida,
    • Michal Levin,
    • and Falk Butter
    Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
    ...for peptide identification. (E) Visualization of the new C. elegans gene F54D10.10 via the Integrative Genomics Viewer (IGV) (Thorvaldsdóttir et al. 2013) aligned to the C. elegans sequence. Presented are read coverage (gray peak track), ORF structure (black bar; thick bar represents translated region...
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