Complete genome sequence of Staphylococcus casei strain DSM 15096

References

1. Place RBE, Hiestand D, Burri S, Teuber M. Staphylococcus succinus subsp. casei subsp. nov., a dominant isolate from a surface ripened cheese. Syst Appl Microbiol 2002; 25:353–359 [View Article] [PubMed]
   [Google Scholar]
2. Madhaiyan M, Wirth JS, Saravanan VS. Phylogenomic analyses of the Staphylococcaceae family suggest the reclassification of five species within the genus Staphylococcus as heterotypic synonyms, the promotion of five subspecies to novel species, the taxonomic reassignment of five Staphylococcus species to Mammaliicoccus gen. nov., and the formal assignment of Nosocomiicoccus to the family Staphylococcaceae. Int J Syst Evol Microbiol 2020; 70:5926–5936 [View Article] [PubMed]
   [Google Scholar]
3. Oren A, Garrity GM. Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 70, part 11 of the IJSEM. Int J Syst Evol Microbiol 2021; 71:71 [View Article] [PubMed]
   [Google Scholar]
4. Cole K, Foster D, Russell JE, Golubchik T, Llewelyn M et al. Draft genome sequences of 64 type strains of 50 species and 25 subspecies of the genus Staphylococcus Rosenbach 1884. Microbiol Resour Announc 2019; 8:e00062-19 [View Article] [PubMed]
   [Google Scholar]
5. Wick RR. Porechop. n.d https://github.com/rrwick/Porechop accessed 1 April 2023
6. Wick RR. Filtlong. n.d https://github.com/rrwick/Filtlong accessed 1 April 2023
7. Kolmogorov M, Bickhart DM, Behsaz B, Gurevich A, Rayko M et al. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat Methods 2020; 17:1103–1110 [View Article] [PubMed]
   [Google Scholar]
8. Vaser R, Sović I, Nagarajan N, Šikić M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res 2017; 27:737–746 [View Article] [PubMed]
   [Google Scholar]
9. Oxford Nanopore Technologies Medaka. n.d https://github.com/nanoporetech/medaka accessed 1 April 2023
10. Huang Y-T, Liu P-Y, Shih P-W. Homopolish: a method for the removal of systematic errors in nanopore sequencing by homologous polishing. Genome Biol 2021; 22:95 [View Article] [PubMed]
    [Google Scholar]
11. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
    [Google Scholar]
12. Joshi NA, Fass JN. Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files. n.d https://github.com/najoshi/sickle accessed 1 April 2023
13. Wick RR, Holt KE. Polypolish: short-read polishing of long-read bacterial genome assemblies. PLoS Comput Biol 2022; 18:e1009802 [View Article] [PubMed]
    [Google Scholar]
14. Zimin AV, Salzberg SL. The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies. PLoS Comput Biol 2020; 16:e1007981 [View Article] [PubMed]
    [Google Scholar]
15. Hu J, Fan J, Sun Z, Liu S, Berger B. NextPolish: a fast and efficient genome polishing tool for long-read assembly. Bioinformatics 2020; 36:2253–2255 [View Article] [PubMed]
    [Google Scholar]
16. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
17. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
    [Google Scholar]