Scalable sequence database search using partitioned aggregated Bloom comb trees

por Marchet, Camille, Limasset, Antoine
Publicado 2023

A survey of mapping algorithms in the long-reads era

por Sahlin, Kristoffer, Baudeau, Thomas, Cazaux, Bastien, Marchet, Camille
Publicado 2023

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

por Marchet, Camille, Iqbal, Zamin, Gautheret, Daniel, Salson, Mikaël, Chikhi, Rayan
Publicado 2020

Scalable long read self-correction and assembly polishing with multiple sequence alignment

por Morisse, Pierre, Marchet, Camille, Limasset, Antoine, Lecroq, Thierry, Lefebvre, Arnaud
Publicado 2021

Data structures based on k-mers for querying large collections of sequencing data sets

por Marchet, Camille, Boucher, Christina, Puglisi, Simon J., Medvedev, Paul, Salson, Mikaël, Chikhi, Rayan
Publicado 2021

ELECTOR: evaluator for long reads correction methods

por Marchet, Camille, Morisse, Pierre, Lecompte, Lolita, Lefebvre, Arnaud, Lecroq, Thierry, Peterlongo, Pierre, Limasset, Antoine
Publicado 2019

De novo clustering of long reads by gene from transcriptomics data

por Marchet, Camille, Lecompte, Lolita, Silva, Corinne Da, Cruaud, Corinne, Aury, Jean-Marc, Nicolas, Jacques, Peterlongo, Pierre
Publicado 2019

Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads

por Lima, Leandro, Sinaimeri, Blerina, Sacomoto, Gustavo, Lopez-Maestre, Helene, Marchet, Camille, Miele, Vincent, Sagot, Marie-France, Lacroix, Vincent
Publicado 2017

A de novo approach to disentangle partner identity and function in holobiont systems

por Meng, Arnaud, Marchet, Camille, Corre, Erwan, Peterlongo, Pierre, Alberti, Adriana, Da Silva, Corinne, Wincker, Patrick, Pelletier, Eric, Probert, Ian, Decelle, Johan, Le Crom, Stéphane, Not, Fabrice, Bittner, Lucie
Publicado 2018

Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data

por Benoit-Pilven, Clara, Marchet, Camille, Chautard, Emilie, Lima, Leandro, Lambert, Marie-Pierre, Sacomoto, Gustavo, Rey, Amandine, Cologne, Audric, Terrone, Sophie, Dulaurier, Louis, Claude, Jean-Baptiste, Bourgeois, Cyril F., Auboeuf, Didier, Lacroix, Vincent
Publicado 2018

SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence

por Lopez-Maestre, Hélène, Brinza, Lilia, Marchet, Camille, Kielbassa, Janice, Bastien, Sylvère, Boutigny, Mathilde, Monnin, David, Filali, Adil El, Carareto, Claudia Marcia, Vieira, Cristina, Picard, Franck, Kremer, Natacha, Vavre, Fabrice, Sagot, Marie-France, Lacroix, Vincent
Publicado 2016

Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

por Le Bras, Yvan, Collin, Olivier, Monjeaud, Cyril, Lacroix, Vincent, Rivals, Éric, Lemaitre, Claire, Miele, Vincent, Sacomoto, Gustavo, Marchet, Camille, Cazaux, Bastien, Zine El Aabidine, Amal, Salmela, Leena, Alves-Carvalho, Susete, Andrieux, Alexan, Uricaru, Raluca, Peterlongo, Pierre
Publicado 2016

Critical Assessment of Metagenome Interpretation: the second round of challenges

por Meyer, Fernando, Fritz, Adrian, Deng, Zhi-Luo, Koslicki, David, Lesker, Till Robin, Gurevich, Alexey, Robertson, Gary, Alser, Mohammed, Antipov, Dmitry, Beghini, Francesco, Bertrand, Denis, Brito, Jaqueline J., Brown, C. Titus, Buchmann, Jan, Buluç, Aydin, Chen, Bo, Chikhi, Rayan, Clausen, Philip T. L. C., Cristian, Alexandru, Dabrowski, Piotr Wojciech, Darling, Aaron E., Egan, Rob, Eskin, Eleazar, Georganas, Evangelos, Goltsman, Eugene, Gray, Melissa A., Hansen, Lars Hestbjerg, Hofmeyr, Steven, Huang, Pingqin, Irber, Luiz, Jia, Huijue, Jørgensen, Tue Sparholt, Kieser, Silas D., Klemetsen, Terje, Kola, Axel, Kolmogorov, Mikhail, Korobeynikov, Anton, Kwan, Jason, LaPierre, Nathan, Lemaitre, Claire, Li, Chenhao, Limasset, Antoine, Malcher-Miranda, Fabio, Mangul, Serghei, Marcelino, Vanessa R., Marchet, Camille, Marijon, Pierre, Meleshko, Dmitry, Mende, Daniel R., Milanese, Alessio, Nagarajan, Niranjan, Nissen, Jakob, Nurk, Sergey, Oliker, Leonid, Paoli, Lucas, Peterlongo, Pierre, Piro, Vitor C., Porter, Jacob S., Rasmussen, Simon, Rees, Evan R., Reinert, Knut, Renard, Bernhard, Robertsen, Espen Mikal, Rosen, Gail L., Ruscheweyh, Hans-Joachim, Sarwal, Varuni, Segata, Nicola, Seiler, Enrico, Shi, Lizhen, Sun, Fengzhu, Sunagawa, Shinichi, Sørensen, Søren Johannes, Thomas, Ashleigh, Tong, Chengxuan, Trajkovski, Mirko, Tremblay, Julien, Uritskiy, Gherman, Vicedomini, Riccardo, Wang, Zhengyang, Wang, Ziye, Wang, Zhong, Warren, Andrew, Willassen, Nils Peder, Yelick, Katherine, You, Ronghui, Zeller, Georg, Zhao, Zhengqiao, Zhu, Shanfeng, Zhu, Jie, Garrido-Oter, Ruben, Gastmeier, Petra, Hacquard, Stephane, Häußler, Susanne, Khaledi, Ariane, Maechler, Friederike, Mesny, Fantin, Radutoiu, Simona, Schulze-Lefert, Paul, Smit, Nathiana, Strowig, Till, Bremges, Andreas, Sczyrba, Alexander, McHardy, Alice Carolyn
Publicado 2022