The microsporidian, Brachiola algerae, for which the size of the genome is estimated at 10 Mb, can be grown in cell culture. Based on the experience and success of the sequencing of the complete genome of E. cuniculi a similar strategy is proposed:

• Production of parasites in cell cultures of human fibroblasts (HFF);
• Purification of resistant forms (spores);
• Elimination of contaminating DNA from host cells by treatment with DNAse (the spore wall protects the DNA of the parasite);
• Purification of parasite DNA (utilization of of the natural property of devagination of the invasion apparatus, leading to release of the DNA of the parasite);
• Construction of two plasmid libraries (inserts of 3 and 10 kb) and a miniBAC library (inserts of about 25 kb);
• Sequencing of recombinant clones (7-8 genome equivalents);
• Assembly;
• Finishing (resequencing of poor-quality regions, or regions with insufficient coverage as well as missing regions);
• Validation of the final assembly by restriction endonuclease analysis of DNA from mini-BACs;
• Annotation.