Searching journal content for articles similar to Sahlin 31 (11): 2080.

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  1. Method: Entropy predicts sensitivity of pseudorandom seeds
    • Benjamin Dominik Maier and
    • Kristoffer Sahlin
    Genome Res. July 2023 33: 1162-1174; Published in Advance May 22, 2023, doi:10.1101/gr.277645.123
    .... A k-mer that is shared by two sequences implies an identical region of size k, and with appropriate length on k, we may detect similar but nonidentical regions through shared k-mers. Some of the reasons that k-mers are often used for sequence similarity detection is because they are fast to construct...
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  2. Method: Accurate short-read alignment through r-index-based pangenome indexing
    • Rahul Varki,
    • Massimiliano Rossi,
    • Eddie Ferro,
    • Marco Oliva,
    • Erik Garrison,
    • Ben Langmead,
    • and Christina Boucher
    Genome Res. July 2025 35: 1609-1620; Published in Advance June 12, 2025, doi:10.1101/gr.279858.124
    ..., the number runs in the BWT grows sublinearly, as repetitive regions of the pan only extend existing runs rather than increase their number (Boucher et al. 2018; Kuhnle et al. 2020). The r-index addresses the space complexity of the FM-index by leveraging the pan's repetitiveness, similar to graph...
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  3. Method: Aligning distant sequences to graphs using long seed sketches
    • Amir Joudaki,
    • Alexandru Meterez,
    • Harun Mustafa,
    • Ragnar Groot Koerkamp,
    • André Kahles,
    • and Gunnar Rätsch
    Genome Res. July 2023 33: 1208-1217; Published in Advance April 18, 2023, doi:10.1101/gr.277659.123
    ..., Hayes W, Hunt BR, Mount SM, Yorke JA. 2004. Reducing storage requirements for biological sequence comparison. Bioinformatics 20: 3363–3369. doi:10.1093/bioinformatics/bth408 ↵Sahlin K. 2021. Effective sequence similarity detection with strobemers. Genome Res 31: 2080–2094. doi:10.1101/gr.275648...
  4. Method: Efficient mapping of accurate long reads in minimizer space with mapquik
    • Bariş Ekim,
    • Kristoffer Sahlin,
    • Paul Medvedev,
    • Bonnie Berger,
    • and Rayan Chikhi
    Genome Res. July 2023 33: 1188-1197; Published in Advance June 30, 2023, doi:10.1101/gr.277679.123
    ...in length with a ≤1% error rate. High-quality long reads have been used to accurately assemble s (Kolmogorov et al. 2019; Nurk et al. 2020; Ekim et al. 2021; Bankevich et al. 2022), complete the human (Nurk et al. 2022), accurately detect small variants in challenging genomic regions (Olson et al. 2022...
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