A method for isolating fragments of genomic DNA regions of interest using an electrophoresis cassette comprising: loading a sample containing particles having high-molecular-weight DNA in a first well of a gel matrix of an electrophoresis cassette; loading a lysis reagent into a second well of the gel matrix of the cassette; applying an electrophoretic field to the gel matrix such that: the lysis reagent is delivered to the first well so as to lyse the particles and release the HMW DNA from the particles; cellular components are electrophoresed from the first well; and the HMW DNA are removed from the particles and trapped in a wall of the first well; emptying and refilling the first well with a custom CRISPR-Cas9 cleavage reagent configured to cleave at specific DNA sequences within the HMW DNA so as to liberate defined segments of the DNA as fragments of reduced size; incubating the cassette at a suitable temperature for a suitable period of time to allow efficient cleavage of the HMW DNA; subjecting the gel matrix to an electrophoretic field, the field being configured to move and thereby separate the DNA fragments from uncleaved DNA of the HMW DNA which remains substantially immobile; and isolating the electrophoretically separated DNA fragments from the gel matrix. loading a sample containing particles having high-molecular-weight DNA in a first well of a gel matrix of an electrophoresis cassette; loading a lysis reagent into a second well of the gel matrix of the cassette; applying an electrophoretic field to the gel matrix such that: the lysis reagent is delivered to the first well so as to lyse the particles and release the HMW DNA from the particles; cellular components are electrophoresed from the first well; and the HMW DNA are removed from the particles and trapped in a wall of the first well; emptying and refilling the first well with a custom CRISPR-Cas9 cleavage reagent configured to cleave at specific DNA sequences within the HMW DNA so as to liberate defined segments of the DNA as fragments of reduced size; incubating the cassette at a suitable temperature for a suitable period of time to allow efficient cleavage of the HMW DNA; subjecting the gel matrix to an electrophoretic field, the field being configured to move and thereby separate the DNA fragments from uncleaved DNA of the HMW DNA which remains substantially immobile; and isolating the electrophoretically separated DNA fragments from the gel matrix. the lysis reagent is delivered to the first well so as to lyse the particles and release the HMW DNA from the particles; cellular components are electrophoresed from the first well; and the HMW DNA are removed from the particles and trapped in a wall of the first well; emptying and refilling the first well with a custom CRISPR-Cas9 cleavage reagent configured to cleave at specific DNA sequences within the HMW DNA so as to liberate defined segments of the DNA as fragments of reduced size; incubating the cassette at a suitable temperature for a suitable period of time to allow efficient cleavage of the HMW DNA; subjecting the gel matrix to an electrophoretic field, the field being configured to move and thereby separate the DNA fragments from uncleaved DNA of the HMW DNA which remains substantially immobile; and isolating the electrophoretically separated DNA fragments from the gel matrix.