Abstract: Various short reads can be grouped and identified as coming from a same long DNA fragment (e.g., by using wells with a relatively low-concentration of DNA). A histogram of the genomic coverage of a group of short reads can provide the edges of the corresponding long fragment (pulse). The knowledge of these pulses can provide an ability to determine the haploid genome and to identify structural variations.

Abstract: A method of illumination and illumination apparatus are provided in a biochip reader. Illumination is provided by a non-collimated laser source or a light emitting diode (LED). The light is directed to opposing sides of a glass substrate by a pair of optical fiber bundles. The glass substrate carries a bioarray. Each of the optical fiber bundles are splayed out to make a fan, the fan being one fiber thick and defining a line of optical fiber faces. This process randomizes any non-uniformity in the illumination source, creating a more uniform illumination source. A respective divergent diffuser engages each row of optical fiber faces coupling and diffusing light substantially evenly through the opposing sides of the glass substrate to illuminate the bioarray supported by the glass substrate. The glass substrate functions as a secondary light guide. The divergent diffusers separate the optical fiber faces from the edges of the glass substrate, protecting the optical fibers from mechanical damage.

Abstract: An automated multicolor fluorescent microscope of the invention includes thermostatic and thermal cycling capability with a wide temperature range, such as a range between ?40 to 110 Celsius degrees, and precision of temperature setting and independency of ambient conditions, wide area of observation, high uniformity of illumination and includes capability to change emission and excitation filters automatically and independently.

Abstract: A method of illumination and illumination apparatus are provided in a biochip reader. Illumination is provided by a non-collimated laser source or a light emitting diode (LED). The light is directed to opposing sides of a glass substrate by a pair of optical fiber bundles. The glass substrate carries a bioarray. Each of the optical fiber bundles are splayed out to make a fan, the fan being one fiber thick and defining a line of optical fiber faces. This process randomizes any non-uniformity in the illumination source, creating a more uniform illumination source. A respective divergent diffuser engages each row of optical fiber faces coupling and diffusing light substantially evenly through the opposing sides of the glass substrate to illuminate the bioarray supported by the glass substrate. The glass substrate functions as a secondary light guide. The divergent diffusers separate the optical fiber faces from the edges of the glass substrate, protecting the optical fibers from mechanical damage.

Abstract: A method of illumination and illumination apparatus are provided in a biochip reader. Illumination is provided by a non-collimated laser source or a light emitting diode (LED). The light is directed to opposing sides of a glass substrate by a pair of optical fiber bundles. The glass substrate carries a bioarray. Each of the optical fiber bundles are splayed out to make a fan, the fan being one fiber thick and defining a line of optical fiber faces. This process randomizes any non-uniformity in the illumination source, creating a more uniform illumination source. A respective divergent diffuser engages each row of optical fiber faces coupling and diffusing light substantially evenly through the opposing sides of the glass substrate to illuminate the bioarray supported by the glass substrate. The glass substrate functions as a secondary light guide. The divergent diffusers separate the optical fiber faces from the edges of the glass substrate, protecting the optical fibers from mechanical damage.