The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time-an ultra-deep approach, PLoS Comput. Biol, vol.6, 2010. ,
Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data, BMC Genom, vol.15, p.264, 2014. ,
URL : https://hal.archives-ouvertes.fr/inserm-00975719
Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus, pp.736-778, 2013. ,
, Emerg. Infect. Dis, vol.19
Complete genome sequences of four novel human coronavirus OC43 isolates associated with severe acute respiratory infection (e00452-18), Genome Announc, vol.6, 2018. ,
CD-HIT: accelerated for clustering the nextgeneration sequencing data, Bioinformatics, vol.28, pp.3150-3152, 2012. ,
Use of genome sequencing to identify hepatitis C virus transmission in a renal healthcare setting, J. Hosp. Infect, vol.96, pp.157-162, 2017. ,
Clinical and biological insights from viral genome sequencing, Nat. Rev. Microbiol, vol.15, pp.183-192, 2017. ,
Use of whole-genome sequencing in the investigation of a nosocomial influenza virus outbreak, J. Infect. Dis, vol.218, pp.1485-1489, 2018. ,
CAP3: a DNA sequence assembly program, Genome Res, vol.9, pp.868-877, 1999. ,
CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing, BMC Bioinforma, vol.15, 2014. ,
Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet. J, vol.17, p.10, 2011. ,
Recent advances in inferring viral diversity from high-throughput sequencing data, Virus Res, vol.239, pp.17-32, 2017. ,
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples, Nat. Protoc, vol.12, pp.1261-1276, 2017. ,
Evaluation of three commercial multiplex assays for the detection of respiratory viral infections, J. Virol. Methods, vol.248, pp.39-43, 2017. ,
Human respiratory coronavirus OC43: genetic stability and neuroinvasion, J. Virol, vol.78, pp.8824-8834, 2004. ,
Complete genome sequence of human coronavirus OC43 isolated from Mexico, pp.1256-1272, 2016. ,
Fulllength genome characterization and genetic relatedness analysis of hepatitis A virus outbreak strains associated with acute liver failure among children, J. Med. Virol, vol.86, pp.202-208, 2014. ,
Complete genomic sequence of human coronavirus OC43: molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event, J. Virol, vol.79, pp.1595-1604, 2005. ,
, Virology, vol.531, pp.141-148, 2019.