An article published in BMCBioInformatics presents Genofunc: a toolkit offering a range of command line orientated functions for processing of raw virus genome sequences into aligned and annotated data ready for analysis.
Although Genofunc was written originally written for processing HIV genome sequences, the package can be easily utilised for other viral sequences with a given reference genome. This is shown through the benchmarking test of different viral datasets against another annotation tool Geneious and comparable to the annotation information on GenBank/Los Alamos.
We believe that based on our case study, Genofunc could be easily used on all viruses for the annotation and identification of gene features especially suitable for processing large raw sequence datasets. The setup of the pipeline using Genofunc in this case study also showed efficiency and simplicity in annotating and extracting key genomic regions from raw sequences which can be used in all forms of applications.
In summary, Genofunc is a single command line toolkit suitable for constructing an automated pipeline to process large raw virus sequence datasets efficiently and readily for large scaled phylogenetics. Genofunc is open source and available with documentation atAll data used in this research can be found on the Los Alamos HIV database found at
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