References
- Levy SE , MyersRM. Advancements in next-generation sequencing. Annu. Rev. Genomics Hum. Genet.17, 95–115 (2016).
- Buermans HP , den DunnenJT. Next generation sequencing technology: advances and applications. Biochim. Biophys. Acta.1842(10), 1932–1941 (2014).
- Reuter JA , SpacekDV, SnyderMP. High-throughput sequencing technologies. Mol. Cell58(4), 586–597 (2015).
- Bentley DR , BalasubramanianS, SwerdlowHPet al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature456(7218), 53–59 (2008).
- Rothberg JM , HinzW, RearickTMet al. An integrated semiconductor device enabling non-optical genome sequencing. Nature475(7356), 348–352 (2011).
- Head SR , KomoriHK, LaMereSAet al. Library construction for next-generation sequencing: overviews and challenges. BioTechniques56(2), 61–77 (2014).
- Zhao G , LiJ, HuT, WeiH, GuanY. Realizing directional cloning using sticky ends produced by 3′-5′ exonuclease of Klenow fragment. J. Biosci.38(5), 857–866 (2013).
- Quail MA , KozarewaI, SmithFet al. A large genome center's improvements to the Illumina sequencing system. Nat. Methods5(12), 1005–1010 (2008).
- Zheng Z , AdvaniA, MeleforsÖet al. Titration-free 454 sequencing using Y adapters. Nat. Protoc.6(9), 1367–1376 (2011).
- Roche . Multiplex Identifier (MID) Adaptors for Rapid Library Preparations. In: Technical Bulletin GS FLX System & GS Junior System.8–9 (2010).
- Wylezich C , PapaA, BeerM, HöperD. A versatile sample processing workflow for metagenomic pathogen detection. Sci. Rep.8(1), 13108 (2018).
- Dumousseau M , RodriguezN, JutyN, LeNovère N. MELTING, a flexible platform to predict the melting temperatures of nucleic acids. BMC Bioinformatics13(1), 101 (2012).
- Afgan E , BakerD, BatutBet al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res.46(W1), W537–W544 (2018).
- Babraham Bioinformatics. FastQC. http://www.bioinformatics.babraham.ac.uk/projects/fastqc
- GitHub . vsbuffalo/qrqc. http://github.com/vsbuffalo/qrqc
- RStudio . www.rstudio.com
- The R Project for Statistical Computing . www.R-project.org
- Alseth I , DalhusB, BjøråsM. Inosine in DNA and RNA. Curr. Opin. Genet. Dev.26, 116–123 (2014).
- Spitzer S , EcksteinF. Inhibition of deoxyribonucleases by phosphorothioate groups in oligodeoxyribonucleotides. Nucleic Acids Res.16(24), 11691–11704 (1988).
- Vosberg HP , EcksteinF. Effect of deoxynucleoside phosphorothioates incorporated in DNA on cleavage by restriction enzymes. J. Biol. Chem.257(11), 6595–6599 (1982).
- Dabney J , MeyerM. Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. BioTechniques52(2), 87–94 (2012).
- Kozarewa I , NingZ, QuailMA, SandersMJ, BerrimanM, TurnerDJ. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat. Methods6(4), 291–295 (2009).
- Forth LF , ScholesSFE, PesaventoPAet al. Novel picornavirus in lambs with severe encephalomyelitis. Emerg. Infect. Dis.25(5), 963–967 (2019).