A little more information will be helpful in answering. Will you be doing targeted sequencing (e.g. AmpliSeq - ion torrent or TruSeq Cancer Panel) Will your DNA of interest be intact from tissue or cells or from FFPE? If FFPE will you first measure the percent amplifiable using a PCR method such as Fluidigm's FTH1 assay from their ADP-29 (Advance Development Protocol)?