Remote DNA Sequencing and Analysis; Nanopore sequencing, FPGA boards and a fortunate Epiphany
summary
Portable nanopore MinION sequencing gives long but noisy reads — basecalling sits near ~85% accuracy and recent yields reach ~8 Gb (roughly 2–3× human coverage), so real-time analysis matters. Analog squiggles move from HMMs to LSTM basecallers for better context, but cloud basecalling cost prompted FPGA/offline options. Experiments with an Epiphany 16‑core board show only marginal speedup versus its ARM and ARM is ~2000× too slow for real‑time, so the custom FPGA/path to a truly portable, working basecaller remains unfinished but educational.
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chapters (8)
- 0:00Start
- 0:06Alexis Luca Tini
- 2:30First Portable Dna Sequencer
- 4:29Main Frontiers of Nanopore Sequencing
- 6:57The Limitations on Portable Sequencing
- 9:28Hidden Markov Model
- 15:29What Is an Fpga
- 18:26Programming an Fpga
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