These extraction protocols describe two methods for harvesting DNA from rabbit muscle, as an example of mammalian muscle. It is recommended to use the QIAGEN Genomic-tip 100/G, either following the standard protocol or by performing the tissue lysis with ATL buffer. We found that the use of ATL buffer produced a sample which generated fewer short reads compared with the sample extracted using the standard protocol, although the read N50 value was slightly higher when following the standard protocol. We recommend the use of SPRI size selection prior to sequencing. The sequencing performance was assessed using the Ligation Sequencing Kit. To obtain more sequencing data from this sample, users may find that their experiments would benefit from a flow cell wash step.