KISSPLICE: de-novo calling alternative splicing events from rna-seq data, BMC Bioinforma, vol.13, issue.6, p.5, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00784407
Reference-free detection of isolated SNPs, Nucleic Acids Research, vol.43, issue.2, 2015. ,
DOI : 10.1093/nar/gku1187
URL : https://hal.archives-ouvertes.fr/hal-01083715
Mapping-Free and Assembly-Free Discovery of Inversion Breakpoints from Raw NGS Reads, Algorithms for Computational Biology. Tarragona, 2015. ,
DOI : 10.1007/978-3-319-07953-0_10
URL : https://hal.archives-ouvertes.fr/hal-01063157
Commet: Comparing and combining multiple metagenomic datasets, 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) ,
DOI : 10.1109/BIBM.2014.6999135
URL : https://hal.archives-ouvertes.fr/hal-01080050
LoRDEC: accurate and efficient long read error correction, Bioinformatics, vol.30, issue.24 ,
DOI : 10.1093/bioinformatics/btu538
URL : https://hal.archives-ouvertes.fr/lirmm-01100451
Galaxy: A platform for interactive large-scale genome analysis, Genome Research, vol.15, issue.10, pp.1451-1455, 2005. ,
DOI : 10.1101/gr.4086505
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences, Genome Biology, vol.11, issue.8, p.86, 2010. ,
DOI : 10.1186/gb-2010-11-8-r86
Galaxy: A Web-Based Genome Analysis Tool for Experimentalists, Curr Protoc Mol Biol, vol.19, pp.201019-201029 ,
DOI : 10.1002/0471142727.mb1910s89
https://www.e-biogenouest.org/groups/guggo. Accessed date 23, 2015. ,
GATB: Genome Assembly & Analysis Tool Box, Bioinformatics, vol.30, issue.20, pp.2959-961, 2014. ,
DOI : 10.1093/bioinformatics/btu406
URL : https://hal.archives-ouvertes.fr/hal-01088571
Space-efficient and exact de Bruijn graph representation based on a Bloom filter, Algorithms for Molecular Biology, vol.8, issue.1, p.22, 2013. ,
DOI : 10.1101/gr.131383.111
URL : https://hal.archives-ouvertes.fr/hal-00753930
Using cascading bloom filters to improve the memory usage for de brujin graphs, Algorithm Mol Biol, vol.9, issue.2, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-00824697
Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nature Biotechnology, vol.30, issue.7, pp.644-52, 2011. ,
DOI : 10.1101/GR.229202. ARTICLE PUBLISHED ONLINE BEFORE MARCH 2002
Navigating in a Sea of Repeats in RNA-seq without Drowning, 14th International Workshop on Algorithms in Bioinformatics (WABI), pp.82-96, 2014. ,
DOI : 10.1007/978-3-662-44753-6_7
URL : https://hal.archives-ouvertes.fr/hal-01079947
Hybrid error correction and de novo assembly of single-molecule sequencing reads, Nature Biotechnology, vol.13, issue.7, pp.693-700, 2012. ,
DOI : 10.1186/gb-2004-5-2-r12
A hybrid approach for the automated finishing of bacterial genomes, Nature Biotechnology, vol.17, issue.7, pp.701-708, 2012. ,
DOI : 10.1007/BF01386390
Improving PacBio Long Read Accuracy by Short Read Alignment, PLoS ONE, vol.7, issue.10, p.46679, 2012. ,
DOI : 10.1371/journal.pone.0046679.s002
Cerulean: A Hybrid Assembly Using High Throughput Short and Long Reads, LNCS, pp.349-63, 2013. ,
DOI : 10.1007/978-3-642-40453-5_27
Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity, Nucleic Acids Research, vol.37, issue.15, p.104, 2009. ,
DOI : 10.1093/nar/gkp492
URL : https://hal.archives-ouvertes.fr/hal-00452377
STAR: ultrafast universal RNA-seq aligner, Bioinformatics, vol.29, issue.1, pp.15-21, 2013. ,
DOI : 10.1093/bioinformatics/bts635
Ensembl 2014, Nucleic Acids Research, vol.42, issue.D1, pp.749-55, 2014. ,
DOI : 10.1093/nar/gkt1196
Whole Genome, Whole Population Sequencing Reveals That Loss of Signaling Networks Is the Major Adaptive Strategy in a Constant Environment, PLoS Genetics, vol.20, issue.103 ,
DOI : 10.1371/journal.pgen.1003972.s009
Accessing the Soil Metagenome for Studies of Microbial Diversity, Applied and Environmental Microbiology, vol.77, issue.4, pp.1315-1324, 2011. ,
DOI : 10.1128/AEM.01526-10
URL : https://hal.archives-ouvertes.fr/hal-00579312
The metagenomics RAST server ??? a public resource for the automatic phylogenetic and functional analysis of metagenomes, BMC Bioinformatics, vol.9, issue.1, pp.386-396, 2008. ,
DOI : 10.1186/1471-2105-9-386
Structure, fluctuation and magnitude of a natural grassland soil metagenome, The ISME Journal, vol.64, issue.9, pp.1677-1687, 2012. ,
DOI : 10.1038/nrmicro2119
URL : https://hal.archives-ouvertes.fr/hal-00747243
ABySS: A parallel assembler for short read sequence data, Genome Research, vol.19, issue.6, pp.1117-1123, 2009. ,
DOI : 10.1101/gr.089532.108
QUAST: quality assessment tool for genome assemblies, Bioinformatics, vol.29, issue.8, pp.1072-1075, 2013. ,
DOI : 10.1093/bioinformatics/btt086
https://wiki.galaxyproject.org. Accessed date 23, 2015. ,
Integrating new visualization tool in galaxy, Galaxy Community Conference 2014, 2014. ,
http://galaxy.genouest.org/. Accessed date 23, 2015. ,
Towards a life sciences virtual research environment: An e-science initiative in western france, JOBIM 2013 Proceedings; 2013. p, pp.97-106 ,
Software and supporting data for Colib'read on Galaxy. GigaScience Database ,
http://downloads.yeastgenome.org/ sequence/S288C_reference/genome_releases. Accessed date 23, 2015. ,