Monday, Feb 3

  • Welcome evening, from 6.30 pm Shamrock pub

Tuesday, Feb 4 Inria/Irisa Campus de Beaulieu - Room Petri/Turing

  • 9:15 Welcome all - few technical information

  • 9:30 Cost-optimal assignment of elements in genome-scale multi-way bucketed Cuckoo hash tables Jens Zentgraf, Henning Timm and Sven Rahmann

  • 10:00 Faster Xenograft Sorting with 3-Way Bucketed Cuckoo Hashing of k-mers Jens Zentgraf and Sven Rahmann

  • 10:30 Coffee break

  • 11:00

    Optical map guided genome assembly

    Miika Leinonen and Leena Salmela

  • 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

  • 12:30 Lunch

  • 13:30 Hierarchical Organization of Syntenic Blocks in Large Genomic Datasets Daniel Doerr

  • 14:00 viaDBG - Fast and accurate approach for viralquasispecies inference Borja Freire, Susana Ladra, José Ramón Paramá and Leena Salmela

  • 14:30 Space-efficient indexing of spaced seeds for accurate overlap computation of raw optical mapping data Riku Walve, Simon Puglisi and Leena Salmela

  • 15:00 Coffee break

  • 15:30 [WIP]

    Computing longest common substring with k mismatches: Theory and practice Garance Gourdel, Tomasz Kociumaka, Jakub Radoszewski and Tatiana Starikovskaya

  • 16:00 [WIP]

    BCash: Best Compressible Hash Antoine Limasset

  • 16:30

    HowDeSBT and Simka wedding. What has been done and what we plan to do Téo Lemane, Paul Medvedev, Pierre Peterlongo

  • 17:00 Time for discussion

  • 19:00 Diner at restaurant “Origines” Hotel Dieu

Tuesday, Feb 5 Inria/Irisa Campus de Beaulieu - Room Petri/Turing

  • 9:00 In-Place Bijective Burrows Wheeler Transformations Dominik Köppl, Daiki Hashimoto, Diptarama Hendrian and Ayumi Shinohara

  • 9:30 Dynamic quasi-minimal perfect hash function for k-mers

    Paola Bonizzoni, Luca Denti, Erik Garrison, Yuri Pirola and Marco Previtali

  • 10:00

    Million sequences indexing Antoine Limasset

  • 10:30 Coffee break

  • 11:00

    REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets

    Camille Marchet, Zamin Iqbal, Mikaël Salson and Rayan Chikhi

  • 11:30 srnaMapper: a mapping tool for short-RNA sequencing Matthias Zytnicki

  • 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

  • 12:30 Lunch

  • 13:30 HASLR: Fast Hybrid Assembly of Long Reads Ehsan Haghshenas, Hossein Asghari, Jens Stoye, Cedric Chauve, Faraz Hach

  • 14:00 Reference independent somatic structural variant call Taiki Yamada, Kenichi Chiba, Nozomi Hasegawa, Keisuke Kataoka, Yuichi Shiraishi and Kana Shimizu

  • 14:30 TBA

    Bastien Cazau

  • 15:00 Final Coffee break and ad libitum discussions