These scripts allow to use blast with bisulfite converted sequences (i.e. sequences in which most Cs have been converted to Ts). To this end, a blast db is created in which all Cs have been replaced by Ts and also in the query sequences all Cs are replaced by Ts. This turned out to work better than using an ambiguity code. The creation of this "converted" blast db is described in createDB. Or you can use the precreated blastDB[25GB]
The intended application is to confirm the species annotation of samples by identifying the "best hits" in the blast nucleotide database for a number of randomly sample reads from reduced representation bisulfite sequencing (RRBS) data. It is intended to work well with the RefFreeDMA pipeline.
Requirements: