, 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
, SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing, Journal of Computational Biology, vol.19, issue.5, pp.455-477, 2012.
DOI : 10.1089/cmb.2012.0021
, Assembling large genomes with single-molecule sequencing and locality-sensitive hashing, Nature Biotechnology, vol.45, issue.6, pp.623-630, 2015.
DOI : 10.1186/gb-2004-5-2-r12
, Variable-Order de Bruijn Graphs, 2015 Data Compression Conference, pp.383-392, 2015.
DOI : 10.1109/DCC.2015.70
, From Indexing Data Structures to de Bruijn Graphs, Proc. CPM 2014, pp.89-99, 2014.
DOI : 10.1007/978-3-319-07566-2_10
URL : https://hal.archives-ouvertes.fr/lirmm-00950983
, Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory, BMC Bioinformatics, vol.13, issue.1, p.238, 2012.
DOI : 10.1145/146637.146650
, Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data, Nature Methods, vol.472, issue.6, pp.563-569, 2013.
DOI : 10.1038/nmeth.2474
, GATB: Genome Assembly & Analysis Tool Box, Bioinformatics, vol.30, issue.20, pp.2959-2961, 2014.
DOI : 10.1093/bioinformatics/btu406
URL : https://hal.archives-ouvertes.fr/hal-01088571
, proovread: large-scale high-accuracy PacBio correction through iterative short read consensus, Bioinformatics, vol.30, issue.21, pp.3004-3011, 2014.
DOI : 10.1093/bioinformatics/btu392
, 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
, One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly, Current Opinion in Microbiology, vol.23, pp.110-120, 2015.
DOI : 10.1016/j.mib.2014.11.014
, Denoising DNA deep sequencing data???high-throughput sequencing errors and their correction, Briefings in Bioinformatics, vol.17, issue.1, pp.154-179, 2016.
DOI : 10.1093/bib/bbv029
, Assessing the performance of the Oxford Nanopore Technologies MinION, Biomolecular Detection and Quantification, vol.3, pp.1-8, 2015.
DOI : 10.1016/j.bdq.2015.02.001
, Multiple sequence alignment using partial order graphs, Bioinformatics, vol.18, issue.3, pp.452-464, 2002.
DOI : 10.1093/bioinformatics/18.3.452
, Genome assembly using Nanopore-guided long and error-free DNA reads, BMC Genomics, vol.29, issue.8, p.327, 2015.
DOI : 10.1186/s12864-015-1519-z
, Jabba: Hybrid Error Correction for Long Sequencing Reads Using Maximal Exact Matches, Proc. WABI 2015, pp.175-188, 2015.
DOI : 10.1007/978-3-662-48221-6_13
, Sequence-specific error profile of Illumina sequencers, Nucleic Acids Research, vol.39, issue.13, p.90, 2011.
DOI : 10.1093/nar/gkr344
, PBSIM: PacBio reads simulator--toward accurate genome assembly, Bioinformatics, vol.29, issue.1, pp.119-121, 2013.
DOI : 10.1093/bioinformatics/bts649
, IDBA ??? A Practical Iterative de Bruijn Graph De Novo Assembler, Proc. RECOMB 2010, pp.426-440, 2010.
DOI : 10.1007/978-3-642-12683-3_28
, LoRDEC: accurate and efficient long read error correction, Bioinformatics, vol.30, issue.24, pp.3506-3514, 2014.
DOI : 10.1093/bioinformatics/btu538
URL : https://hal.archives-ouvertes.fr/lirmm-01100451
, Correcting errors in short reads by multiple alignments, Bioinformatics, vol.27, issue.11, pp.1455-1461, 2011.
DOI : 10.1093/bioinformatics/btr170
, Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform, Nucleic Acids Research, vol.43, issue.6, p.37, 2015.
DOI : 10.1093/nar/gku1341
, A survey of error-correction methods for next-generation sequencing, Briefings in Bioinformatics, vol.14, issue.1, pp.56-66, 2013.
DOI : 10.1093/bib/bbs015