Genetic analysis with pyrosequencing using loop pipetting and a light dependent resistor

A DNA sequencer called LoopSeeq was developed using pyrosequencing chemistry where iterative addition of dNTPs was performed by contact dispensing through a loop pipette and detection of chemiluminescence with inexpensive light sensor LDR for point-of-care applications.

DeepNano-blitz: A Fast Base Caller for MinION Nanopore Sequencers

MotivationOxford Nanopore MinION is a portable DNA sequencer that is marketed as a device that can be deployed anywhere. Current base callers, however, require a powerful GPU to analyze data produced by MinION in real time, which hampers field applications.ResultsWe have developed a fast base caller DeepNano-blitz that can analyze stream from up to two MinION runs in real time using a common laptop CPU (i7-7700HQ), with no GPU requirements. The base caller settings allow trading accuracy for speed and the results can be used for real time run monitoring (i.e. sample composition, barcode balance, species identification, etc.) or pre-filtering of results for more detailed analysis (i.e. filtering out human DNA from human–pathogen runs).Availability and ImplementationDeepNano-blitz has been developed and tested on Linux and is available under MIT license at https://github.com/fmfi-compbio/[email protected]