Did anyone know which tool can calculate the tetranucleotide frequency of fasta file and condust the cluster based on the results.
Im trying to bin my assembled contigs into bins in order to develop draft genome basically following the methodology of a science paper: Hess, M., A. Sczyrba, R. Egan, T.-W. Kim, H. Chokhawala, G. Schroth, S. Luo, et al. “Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen.” Science 331, no. 6016 (January 27, 2011): 463–467.
But I found difficulty when doing the tetranucleotide freq calculation. I do found TETRA, but the software could not handle my dataset with 3G data.
Ive no informatics background, it seems quite simple algorithm. Maybe it had been used in some software package. Please let me know if you know any tool could do this? And hopefully told me about the basic how to, otherwise it is too hard for me to touch into the language. THX a lot.