Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Tizian Schulz and Paul Medvedev. Exact Sketch-Based Read Mapping. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 14:1-14:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{schulz_et_al:LIPIcs.WABI.2023.14, author = {Schulz, Tizian and Medvedev, Paul}, title = {{Exact Sketch-Based Read Mapping}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {14:1--14:19}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-294-5}, ISSN = {1868-8969}, year = {2023}, volume = {273}, editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.14}, URN = {urn:nbn:de:0030-drops-186403}, doi = {10.4230/LIPIcs.WABI.2023.14}, annote = {Keywords: Sequence Sketching, Long-read Mapping, Exact Algorithm, Dynamic Programming} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Amatur Rahman, Yoann Dufresne, and Paul Medvedev. Compression Algorithm for Colored de Bruijn Graphs. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 17:1-17:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{rahman_et_al:LIPIcs.WABI.2023.17, author = {Rahman, Amatur and Dufresne, Yoann and Medvedev, Paul}, title = {{Compression Algorithm for Colored de Bruijn Graphs}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {17:1--17:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-294-5}, ISSN = {1868-8969}, year = {2023}, volume = {273}, editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.17}, URN = {urn:nbn:de:0030-drops-186434}, doi = {10.4230/LIPIcs.WABI.2023.17}, annote = {Keywords: colored de Bruijn graphs, disk compression, k-mer sets, simplitigs, spectrum-preserving string sets} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Leena Salmela. Efficient Solutions to Biological Problems Using de Bruijn Graphs (Invited Talk). In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 1:1-1:2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{salmela:LIPIcs.WABI.2022.1, author = {Salmela, Leena}, title = {{Efficient Solutions to Biological Problems Using de Bruijn Graphs}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {1:1--1:2}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.1}, URN = {urn:nbn:de:0030-drops-170357}, doi = {10.4230/LIPIcs.WABI.2022.1}, annote = {Keywords: de Bruijn graph, variable order de Bruijn graph, genome assembly, sequencing error correction, k-mers} }
Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)
Yoann Dufresne, Chen Sun, Pierre Marijon, Dominique Lavenier, Cedric Chauve, and Rayan Chikhi. A Graph-Theoretic Barcode Ordering Model for Linked-Reads. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 11:1-11:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@InProceedings{dufresne_et_al:LIPIcs.WABI.2020.11, author = {Dufresne, Yoann and Sun, Chen and Marijon, Pierre and Lavenier, Dominique and Chauve, Cedric and Chikhi, Rayan}, title = {{A Graph-Theoretic Barcode Ordering Model for Linked-Reads}}, booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)}, pages = {11:1--11:17}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-161-0}, ISSN = {1868-8969}, year = {2020}, volume = {172}, editor = {Kingsford, Carl and Pisanti, Nadia}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.11}, URN = {urn:nbn:de:0030-drops-128001}, doi = {10.4230/LIPIcs.WABI.2020.11}, annote = {Keywords: DNA sequencing, graph algorithms, linked-reads, interval graphs, cliques} }
Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)
Amatur Rahman, Rayan Chikhi, and Paul Medvedev. Disk Compression of k-mer Sets. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 16:1-16:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@InProceedings{rahman_et_al:LIPIcs.WABI.2020.16, author = {Rahman, Amatur and Chikhi, Rayan and Medvedev, Paul}, title = {{Disk Compression of k-mer Sets}}, booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)}, pages = {16:1--16:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-161-0}, ISSN = {1868-8969}, year = {2020}, volume = {172}, editor = {Kingsford, Carl and Pisanti, Nadia}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.16}, URN = {urn:nbn:de:0030-drops-128057}, doi = {10.4230/LIPIcs.WABI.2020.16}, annote = {Keywords: de Bruijn graphs, compression, k-mer sets, spectrum-preserving string sets} }
Published in: LIPIcs, Volume 78, 28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017)
Massimo Cairo, Paul Medvedev, Nidia Obscura Acosta, Romeo Rizzi, and Alexandru I. Tomescu. Optimal Omnitig Listing for Safe and Complete Contig Assembly. In 28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 78, pp. 29:1-29:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{cairo_et_al:LIPIcs.CPM.2017.29, author = {Cairo, Massimo and Medvedev, Paul and Obscura Acosta, Nidia and Rizzi, Romeo and Tomescu, Alexandru I.}, title = {{Optimal Omnitig Listing for Safe and Complete Contig Assembly}}, booktitle = {28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017)}, pages = {29:1--29:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-039-2}, ISSN = {1868-8969}, year = {2017}, volume = {78}, editor = {K\"{a}rkk\"{a}inen, Juha and Radoszewski, Jakub and Rytter, Wojciech}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2017.29}, URN = {urn:nbn:de:0030-drops-73423}, doi = {10.4230/LIPIcs.CPM.2017.29}, annote = {Keywords: genome assembly, graph algorithm, edge-covering walk, strong bridge} }
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