This is the Linux app named PB-sQF_BacterialTyping whose latest release can be downloaded as PBsQF_Mac.zip. It can be run online in the free hosting provider OnWorks for workstations.
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Probability Binning - signature Quadratic Form, PB-sQF, types unknown sequence to one of the 628 bacterial library genomes which gives the smallest test statistics thus most similar library strain.
The input file is the k-mer counts of the unknown assembled genome sequence or raw short reads file in decimal format generated by KAnalyze developed by P. Audano et al. (https://sourceforge.net/projects/kanalyze/).
The download included the library index, the library name and sample unknowns.
- Calculating test statistics between library and unknown k-mer frequency
- Bacterial sequence typing
This is an application that can also be fetched from https://sourceforge.net/projects/pb-sqf-bacterialtyping/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.