A comparison of the conceptual steps in aCGH and CNV-seq methods. 1. Starting material in both cases is genomic fragments from two genomes. 2. In CNV-seq the fragments are samples and sequenced. 3. Genomic fragments are directly hybridized on to an array. In CNV-seq the mapping is performed by sequence alignment. 4. In microarray the light intensities reflect the number of hybridized fragments. In CNV-seq the number of mapped reads are counted directly. 5. Data analysis, including estimation of copy number ratios, confidence values, etc. 6. Output of the results.