Searching journal content for articles similar to Karasikov et al. 32 (9): 1754.

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  1. 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
    ..., Zimmermann M, Barber C, Rätsch G, Kahles A. 2020. MetaGraph: indexing and analysing nucleotide archives at petabase-scale. bioRxiv doi:10.1101/2020.10.01.322164 ↵Karasikov M, Mustafa H, Rätsch G, Kahles A. 2022. Lossless indexing with counting de Bruijn graphs. Genome Res 32: 1754–1764. doi:10.1101/gr.276607...
  2. 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...
  3. 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
    ...the open-source software graph-gene-caller (ggCaller). ggCaller combines gene prediction, functional annotation, and clustering into a single workflow using population-wide de Bruijn graphs, removing redundancy in gene annotation and resulting in more accurate gene predictions and orthologue clustering. We...
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  4. Resource: Efficient de novo assembly of large genomes using compressed data structures
    • Jared T. Simpson and
    • Richard Durbin
    Genome Res. March 2012 22: 549-556; Published in Advance December 7, 2011, doi:10.1101/gr.126953.111
    ...on de Bruijn graphs, and is simply parallelizable. We demonstrate the error correction and assembly performance of SGA on 1.2 billion sequence reads from a human genome, which we are able to assemble using 54 GB of memory. The resulting contigs are highly accurate and contiguous, while covering 95...
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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
    ...has also been proven to be optimal for lossless filtering of single-base errors (Kucherov et al. 2005; Břinda 2013). For example, with k = 11, the split k–mer would be XXXXX-XXXXX, where X = {A, C, G, T} and “-” is any base. The methods used in SKA2 are demonstrated with an example with k = 11...
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  6. Method: Effective sequence similarity detection with strobemers
    • Kristoffer Sahlin
    Genome Res. November 2021 31: 2080-2094; Published in Advance October 19, 2021, doi:10.1101/gr.275648.121
    ...usage when storing an index with the templates for the reference. Construction of multiple spaced seed patterns has also been presented to allow for matches up to one gap (Burkhardt and Kärkkäinen 2002) or up to some level of mismatches (Pevzner and Waterman 1995; Kucherov et al. 2005).As third...
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  7. Method: Efficient storage of high throughput DNA sequencing data using reference-based compression
    • Markus Hsi-Yang Fritz,
    • Rasko Leinonen,
    • Guy Cochrane,
    • and Ewan Birney
    Genome Res. May 2011 21: 734-740; Published in Advance January 18, 2011, doi:10.1101/gr.114819.110
    ...the ‘‘correct’’ assembled sequence from the fragmented reads from shotgun sequencing. Here, we have used a large-scale de Bruijn graph framework, Cortex (Z Iqbal and M Caccamo, in prep.), to find regions of contiguous sequence in unaligned reads. From a sample of unaligned reads from the NA12878 , which...
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