Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads, PLoS Comput. Biol, vol.13, p.1005595, 2017. ,
NanoPack: visualizing and processing long read sequencing data, Bioinforma. Oxf. Engl, 2018. ,
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation, Genome Res, vol.27, pp.722-736, 2017. ,
Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement, PloS One, vol.9, p.112963, 2014. ,
BUSCO: assessing genome assembly and annotation completeness with single-copy 18 ,
, orthologs. Bioinforma. Oxf. Engl, vol.31, pp.3210-3212, 2015.
Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinforma. Oxf. Engl, vol.25, pp.1754-1760, 2009. ,
The Sequence Alignment/Map format and SAMtools, Bioinforma. Oxf. Engl, vol.25, pp.2078-2079, 2009. ,
Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses, Genome Biol. Evol, vol.7, pp.2010-2022, 2015. ,
mixtools: An R Package for Analyzing Mixture Models, J. Stat. Softw, vol.32, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00384896
Complementarity of statistical treatments to reconstruct worldwide routes of invasion: the case of the Asian ladybird Harmonia axyridis, Mol. Ecol, vol.23, pp.5979-5997, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-02635016
VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing, Genome Res, vol.22, pp.568-576, 2012. ,
Measuring genetic differentiation from Pool-seq data, bioRxiv, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01936905
Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates, Genetics, vol.201, pp.1555-1579, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-02634373
Weight of evidence: A brief survey, Bayesian Stat, vol.2, pp.249-270, 1985. ,
Fast identification and removal of sequence contamination from genomic and metagenomic datasets, PloS One, vol.6, p.17288, 2011. ,
Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinforma. Oxf. Engl, vol.30, pp.2114-2120, 2014. ,
Finished bacterial genomes from shotgun sequence data, Genome Res, vol.22, pp.2270-2277, 2012. ,
Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology, PloS One, vol.7, p.47768, 2012. ,
Versatile and open software for comparing large genomes, Genome Biol, vol.5, p.12, 2004. ,
BLAST+: architecture and applications, BMC Bioinformatics, vol.10, p.421, 2009. ,
Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae), Mol. Ecol. Resour, vol.18, pp.602-619, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02627784
Larval RNAi Applied to the Analysis of Postembryonic Development in the Ladybird Beetle, Harmonia axyridis, J. Insect Biotechnol. Sericology, vol.74, pp.95-102, 2005. ,
Emergence and diversification of fly pigmentation through evolution of a gene regulatory module, Science, vol.339, pp.1423-1426, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00862170
GenomeMatcher: a graphical user interface for DNA sequence comparison, BMC Bioinformatics, vol.9, p.376, 2008. ,
ACT: the Artemis Comparison Tool, Bioinforma. Oxf. Engl, vol.21, pp.3422-3423, 2005. ,
Characterizing the adult and larval transcriptome of the multicolored Asian lady beetle, Harmonia axyridis, PeerJ, vol.4, p.2098, 2016. ,
TopHat: discovering splice junctions with RNA-Seq, Bioinforma. Oxf. Engl, vol.25, pp.1105-1111, 2009. ,
Transcript assembly and quantification by RNA-Seq reveals ,