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Comment by atg_gcg_aca_aca | Hacker News Reader

A few years ago, the sequencing field was really excited for this platform as an alternative/competitor to Illumina. Unfortunately, the MinION platform has never been able to generate enough high-quality data for most eukaryotic sequencing use cases. The MinION still has it's niche... long read sequencing can resolve problematic regions of the genome, and the minION is the only option for rapid sequencing in the field. For production genome sequencing centers though, Illumina's still the dominant tech. Their HiSeq X platform can put out a human genome right about $1k.

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> Their HiSeq X platform can put out a human genome right about $1k.

That's what Illumina will tell you. But that really depends what you mean by "a genome" and what you intend to use it for. Getting anywhere near the quality of the Human Genome Project is not possible.

> Getting anywhere near the quality of the Human Genome Project is not possible.

That is an unrealistic and inappropriate metric to use.

The HiSeq X isn't mean for making new human reference genomes. It's meant for re-sequencing at scale, and speaking from personal experience, it does an incredible job in quality, speed, and cost.

Even if we could reach reference assembly quality with a hiseq run, we wouldn't want to use it that way. Having reference genomes and annotations (hg19 and hg38) means we can compare and contrast individuals from a common foundation. It would increase the cost and time of genome analysis 100 fold if we had to do denovo assemble for each individual sequenced.

I think we should be clear that for $1k you get something that is entirely different than a human genome. It's just a set of short reads that can be mapped onto a reference genome. You can't de novo assemble it, so you won't be able to see a lot of variation. In fact we can't even estimate how much large scale variation there is because all the studies are based on the short reads.

Where do you see PacBio?

While I've been out of the area for almost 3 years now (I sysadmin-supported GS FLX from Roche/454, MiSeq and HiSeq from Illumina, and PGM from IonTorrent), the thing to remember is that each sequencer has it's strengths and weaknesses depending on what you want. Do you want to focus on read length, run time, reads per run, reagent cost, equipment cost, accuracy, etc.

As for pacbio, if I remeber correctly, their cost was low (high equipment cost though) and sequencing was relatively fast, but at a reduction of accuracy. Never dealt with them first hand though.

Niche uses where long-read sequencing is required (denovo assembly, reference improvement, bacterial genomes, whole-isoform transcriptomes. Nanopore is starting to eat into that market, though.

pacbio has this fundamental problem that it's a single molecule process (as does MinION) and deconvoluting errors becomes a problem of unit parallelization.

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