3 ms·

That's very interesting. Do you mind sharing some more details on what those computations are? Where can I learn more about these DNA analysis use cases?

inetknght 7y ago
I've found that Wikipedia has really good high-level information for a lot of the subject matter. For use cases, the business sells direct-to-consumer DNA tests. I've worked on several of the analysis products' softwares. The compute-heavy workload calculates edit distance [0] of short paired-end sequenced DNA [1] vs the human genome [2]. There is open source software to manipulate the FASTA/FASTQ [3] and SAM files [4] and run the calculations [5]. The aligned file is processed in a couple of minutes to genetic variation report [6] which is used for some of the analysis products that were purchased. One popular product will give you a haplogroup [7] which basically tells you where you are in a genetic tree. The relationship estimator uses a different sequencing technology and basically consumes a CSV file from the sequencer's manufacturer. It uses a proprietary algorithm to calculate centimorgans [8]. That then gives relationship estimates between you and other people who've purchased the product. [0]: https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algor... [1]: https://en.wikipedia.org/wiki/Next-generation_sequencing https://en.wikipedia.org/wiki/Next-generation_sequencing [2]: https://en.wikipedia.org/wiki/Reference_genome https://en.wikipedia.org/wiki/Reference_genome [3]: https://en.wikipedia.org/wiki/FASTQ_format https://en.wikipedia.org/wiki/FASTQ_format [4]: https://github.com/samtools/hts-specs https://github.com/samtools/hts-specs [5]: https://en.wikipedia.org/wiki/List_of_sequence_alignment_software https://en.wikipedia.org/wiki/List_of_sequence_alignment_sof... [6]: https://en.wikipedia.org/wiki/Variant_Call_Format https://en.wikipedia.org/wiki/Variant_Call_Format [7]: https://en.wikipedia.org/wiki/Haplogroup https://en.wikipedia.org/wiki/Haplogroup [8]: https://en.wikipedia.org/wiki/Centimorgan https://en.wikipedia.org/wiki/Centimorgan

inetknght 7y ago

I've found that Wikipedia has really good high-level information for a lot of the subject matter. For use cases, the business sells direct-to-consumer DNA tests. I've worked on several of the analysis products' softwares. The compute-heavy workload calculates edit distance [0] of short paired-end sequenced DNA [1] vs the human genome [2]. There is open source software to manipulate the FASTA/FASTQ [3] and SAM files [4] and run the calculations [5]. The aligned file is processed in a couple of minutes to genetic variation report [6] which is used for some of the analysis products that were purchased. One popular product will give you a haplogroup [7] which basically tells you where you are in a genetic tree. The relationship estimator uses a different sequencing technology and basically consumes a CSV file from the sequencer's manufacturer. It uses a proprietary algorithm to calculate centimorgans [8]. That then gives relationship estimates between you and other people who've purchased the product. [0]: https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algor... [1]: https://en.wikipedia.org/wiki/Next-generation_sequencing https://en.wikipedia.org/wiki/Next-generation_sequencing [2]: https://en.wikipedia.org/wiki/Reference_genome https://en.wikipedia.org/wiki/Reference_genome [3]: https://en.wikipedia.org/wiki/FASTQ_format https://en.wikipedia.org/wiki/FASTQ_format [4]: https://github.com/samtools/hts-specs https://github.com/samtools/hts-specs [5]: https://en.wikipedia.org/wiki/List_of_sequence_alignment_software https://en.wikipedia.org/wiki/List_of_sequence_alignment_sof... [6]: https://en.wikipedia.org/wiki/Variant_Call_Format https://en.wikipedia.org/wiki/Variant_Call_Format [7]: https://en.wikipedia.org/wiki/Haplogroup https://en.wikipedia.org/wiki/Haplogroup [8]: https://en.wikipedia.org/wiki/Centimorgan https://en.wikipedia.org/wiki/Centimorgan