Published in: LIPIcs, Volume 265, 21st International Symposium on Experimental Algorithms (SEA 2023)
Diego Díaz-Domínguez, Saska Dönges, Simon J. Puglisi, and Leena Salmela. Simple Runs-Bounded FM-Index Designs Are Fast. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 7:1-7:16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)
@InProceedings{diazdominguez_et_al:LIPIcs.SEA.2023.7, author = {D{\'\i}az-Dom{\'\i}nguez, Diego and D\"{o}nges, Saska and Puglisi, Simon J. and Salmela, Leena}, title = {{Simple Runs-Bounded FM-Index Designs Are Fast}}, booktitle = {21st International Symposium on Experimental Algorithms (SEA 2023)}, pages = {7:1--7:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-279-2}, ISSN = {1868-8969}, year = {2023}, volume = {265}, editor = {Georgiadis, Loukas}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2023.7}, URN = {urn:nbn:de:0030-drops-183579}, doi = {10.4230/LIPIcs.SEA.2023.7}, annote = {Keywords: data structures, efficient algorithms} }
Published in: LIPIcs, Volume 223, 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)
Diego Díaz-Domínguez and Gonzalo Navarro. Efficient Construction of the BWT for Repetitive Text Using String Compression. In 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 29:1-29:18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)
@InProceedings{diazdominguez_et_al:LIPIcs.CPM.2022.29, author = {D{\'\i}az-Dom{\'\i}nguez, Diego and Navarro, Gonzalo}, title = {{Efficient Construction of the BWT for Repetitive Text Using String Compression}}, booktitle = {33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)}, pages = {29:1--29:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-234-1}, ISSN = {1868-8969}, year = {2022}, volume = {223}, editor = {Bannai, Hideo and Holub, Jan}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2022.29}, URN = {urn:nbn:de:0030-drops-161564}, doi = {10.4230/LIPIcs.CPM.2022.29}, annote = {Keywords: BWT, string compression, repetitive text} }
Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)
Travis Gagie, Garance Gourdel, and Giovanni Manzini. Compressing and Indexing Aligned Readsets. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 13:1-13:21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2021)
@InProceedings{gagie_et_al:LIPIcs.WABI.2021.13, author = {Gagie, Travis and Gourdel, Garance and Manzini, Giovanni}, title = {{Compressing and Indexing Aligned Readsets}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {13:1--13:21}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-200-6}, ISSN = {1868-8969}, year = {2021}, volume = {201}, editor = {Carbone, Alessandra and El-Kebir, Mohammed}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.13}, URN = {urn:nbn:de:0030-drops-143660}, doi = {10.4230/LIPIcs.WABI.2021.13}, annote = {Keywords: data compression, compact data structures, FM-index, Burrows-Wheeler Transform, EBWT, XBWT, DNA reads} }
Published in: LIPIcs, Volume 128, 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)
Diego Díaz-Domínguez, Travis Gagie, and Gonzalo Navarro. Simulating the DNA Overlap Graph in Succinct Space. In 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 128, pp. 26:1-26:20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2019)
@InProceedings{diazdominguez_et_al:LIPIcs.CPM.2019.26, author = {D{\'\i}az-Dom{\'\i}nguez, Diego and Gagie, Travis and Navarro, Gonzalo}, title = {{Simulating the DNA Overlap Graph in Succinct Space}}, booktitle = {30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)}, pages = {26:1--26:20}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-103-0}, ISSN = {1868-8969}, year = {2019}, volume = {128}, editor = {Pisanti, Nadia and P. Pissis, Solon}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2019.26}, URN = {urn:nbn:de:0030-drops-104978}, doi = {10.4230/LIPIcs.CPM.2019.26}, annote = {Keywords: Overlap graph, de Bruijn graph, DNA sequencing, Succinct ordinal trees} }
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