For citing correctly in publications the tools used for this analysis the following references should be used:


Ridom SeqSphere+ version 4.0
Jünemann S et al. (2013). Nat Biotechnol. 31:294-6. [PubMed 23563421]


BLAST version 2.2.12 (genome scanning)
Altschul SF et al. (1997). Nucleic Acids Res. 25:3389-402. [PubMed 9254694]


Velvet version 1.1.04 (de novo assembly)
Zerbino DR, Birney E (2008). Genome Res. 18:821-9. [PubMed 18349386]


BWA-SW version 0.6.1/0.6.2 (reference mapping, windows/linux)
Li H, Durbin R (2010). Bioinformatics 26:589-95. [PubMed 20080505]


SPAdes version 3.9.0 (de novo assembly)
Bankevich A, Nurk S et al. (2012). J. Comp. Biol. 19:455-477. [PubMed 22506599]