Program
Monday, Feb 3
- Welcome evening, from 6.30 pm Shamrock pub
Tuesday, Feb 4 Inria/Irisa Campus de Beaulieu - Room Petri/Turing
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9:15 Welcome all - few technical information
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9:30 Cost-optimal assignment of elements in genome-scale multi-way bucketed Cuckoo hash tables Jens Zentgraf, Henning Timm and Sven Rahmann
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10:00 Faster Xenograft Sorting with 3-Way Bucketed Cuckoo Hashing of k-mers Jens Zentgraf and Sven Rahmann
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10:30 Coffee break
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11:00
Optical map guided genome assembly
Miika Leinonen and Leena Salmela
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11:30 (two combined talks) Efficient and scalable representation of k-mer sets using simplitigs and spectrum-preserving string sets
Amatur Rahman, Paul Medvedev, Karel Brinda, Michael Baym and Gregory Kucherov
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12:30 Lunch
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13:30 Hierarchical Organization of Syntenic Blocks in Large Genomic Datasets Daniel Doerr
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14:00 viaDBG - Fast and accurate approach for viralquasispecies inference Borja Freire, Susana Ladra, José Ramón Paramá and Leena Salmela
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14:30 Space-efficient indexing of spaced seeds for accurate overlap computation of raw optical mapping data Riku Walve, Simon Puglisi and Leena Salmela
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15:00 Coffee break
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15:30 [WIP]
Computing longest common substring with k mismatches: Theory and practice Garance Gourdel, Tomasz Kociumaka, Jakub Radoszewski and Tatiana Starikovskaya
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16:00 [WIP]
BCash: Best Compressible Hash Antoine Limasset
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16:30
HowDeSBT and Simka wedding. What has been done and what we plan to do Téo Lemane, Paul Medvedev, Pierre Peterlongo
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17:00 Time for discussion
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19:00 Diner at restaurant “Origines” Hotel Dieu
Tuesday, Feb 5 Inria/Irisa Campus de Beaulieu - Room Petri/Turing
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9:00 In-Place Bijective Burrows Wheeler Transformations Dominik Köppl, Daiki Hashimoto, Diptarama Hendrian and Ayumi Shinohara
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9:30 Dynamic quasi-minimal perfect hash function for k-mers
Paola Bonizzoni, Luca Denti, Erik Garrison, Yuri Pirola and Marco Previtali
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10:00
Million sequences indexing Antoine Limasset
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10:30 Coffee break
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11:00
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets
Camille Marchet, Zamin Iqbal, Mikaël Salson and Rayan Chikhi
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11:30 srnaMapper: a mapping tool for short-RNA sequencing Matthias Zytnicki
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12:00 Shark: fishing in a sample to discard irrelevant RNA-Seq reads Paola Bonizzoni, Tamara Ceccato, Gianluca Della Vedova, Luca Denti, Yuri Pirola, Marco Previtali and Raffaella Rizzi
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12:30 Lunch
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13:30 HASLR: Fast Hybrid Assembly of Long Reads Ehsan Haghshenas, Hossein Asghari, Jens Stoye, Cedric Chauve, Faraz Hach
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14:00 Reference independent somatic structural variant call Taiki Yamada, Kenichi Chiba, Nozomi Hasegawa, Keisuke Kataoka, Yuichi Shiraishi and Kana Shimizu
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14:30 TBA
Bastien Cazau
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15:00 Final Coffee break and ad libitum discussions