We use a Qiagen (formerly Gentra) kit. Catalog #158422. The kit includes an RBC lysis solution as well as a cell lysis solution. We use the RBC lysis solution alone to make "whole cell" preps of Babesia, such as western blot antigen. Or else we follow the procedure to extract genomic DNA.
I am unclear here. I understood you were asking for a method to isolate the parasites themselves, not parasite DNA. We still do not have a good procedure to isolate the parasites away from red blood cells. They get "trapped" by collapsed RBC membranes, so RBC materials are always a contaminant.
If it's DNA you're after, we use Whatman CF11 to remove WBCs and extracellular DNA (Ambrosio, RE et al. 1986. Onderstepoort J. Vet. Res. 53: 179-180) from red cells prior to culture (DNA content of 1 WBC = 1000 parasites). We then use a classic SDS-proteinase K lysis with phenol-chloroform cleanup (Tripp, CA et al. 1989. Exp. Parasitol. 69: 211-225), followed by RNase treatment, re-extraction and re-precipitation. If there is sufficient DNA we will spool the DNA on a glass rod (flamed to eliminate any contamination) following the second set of extractions. It gives us better very large fragment DNA (less shearing) with less contamination. We also use ammonium acetate during DNA precipitations, as it is both equally as effective for precipitation and easier to get rid of than is sodium acetate (Crouse, J and Amorese, D. 1987. Focus 9: 3-6). This combination gave us gDNAs that worked exceptionally well for construction of cosmid libraries of large fragments. Although these procedures are not as convenient as filter-based kits they work very well and provide very clean DNA. Importantly, they are much easier to scale up for large volumes than are filter-based methods.