Overview of Illumina Sequencing by Synthesis Workflow | Standard SBS chemistry
Why Hacker News recommends it
Commenters call it the best visualization of how the most common DNA sequencers work, though it predates newer chemistry.
What it is
Illumina's 3D animation of its sequencing-by-synthesis workflow, from sample preparation and cluster generation to sequencing on a flow cell and data analysis.
Recommended by 1 HN commenters across 1 different months, 2017 to 2019.
What Hacker News said
Recommends shpx · 2017-10 · on “No human genome has ever been completely sequenced”
[this video] is the best visualization of how the most popular type of DNA sequencer works (that I've found). Imagine you have a string of length 3 billion made by randomly choosing from 4 characters. Like this dna = ''.join(random.choices('atgc', weights=[30.9, 29.4, 19.9, 19.8], k=3_234_830_000)) you get to randomly sample 1 billion[3, page 7] overlapping substrings of length 200[3, page 7] with .1% of the characters randomly changed[3, page 8]. Trying to find the original string from this is technically an undecidable problem. If there's a sequence 400 characters long that repeats multiple times, how could you know if it repeats 5 times or 50 times? (this would be unlikely to happen with rando
Cites epistasis · 2019-05 · on “Genomics – A programmer’s guide”
That video describes the process used before NGS was around. These days, using anything with plasmids would be pretty unusual. There are several next generation sequencing technologies: 1) short read - Illumina - dominates most next-generation sequencing 2) long read - nanopore or pacbio. These have very different analysis methods, have measurement errors that are very different, and even have different file formats, etc. Short read is far more common, so you're probably in the "Data Analysis" of this: [this video] But you need to know about the adapters and indices (how multiple samples can be sequenced at the same time). But as another commenter mentions, knowing some particulars about the proj
Cites lkirk · 2019-09 · on “DNA Data Storage: The Entirety of YouTube Could Fit on a Teaspoon”
A sequencing run (at least in the context of Illumina's technology) requires a few very expensive consumable reagents: First being the flowcell (microscope slide that the dna sticks to while being read by a laser), the reagents (containing enzymes with fluorophores and other reagents for amplifying and manipulating DNA), and the actual power consumed by such machinery. This does not factor in prep/lab costs (which can be kept at a minimum with automation, but that also is a high startup cost endeavor). Each sequencing run can take ~1-3 days depending on the format. Edit: this video may be able to explain a little better how this process works: [this video]