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4 replies (most recent on top)
DRAGEN does provide some value for short-read resequencing applications. But without input from former algorithm experts and extracting foundamental ideas from open software and internal pipelines (like GATK etc.), it can't reach current height. Also it's harder and harder to keep balance for cancer applications with exploded parameters. Many users even don't know the best practices with the oversimple online user guide. Alternatives like Sentieon do exist and look healthy.
On the other hand, it's clearer and clearer that long-read assembly is the future for whole genome (which Illumina is eager to lock inside its ecosystem). Just check how simple to assemble a genome with HIFI / ONT UL compared to 10yrs ago. And for single-cell applications, the analysis is more about what one wants to do with those sparse data points downstreams rather than just getting a gene-expression matrix. Don't mention those applications that DRAGEN can‘t cover.
Finally don't forget that we all stand on the shoulders of giants (including those students and researchers). Without those original ideas / implementations on github, you would never figure it out by yourselves.
GATK is very far from high quality industry grade, to whoever the misinformed person making that statement.
Most other bioinformatics software is also total sh*t, written by student for a paper, because all that matter is to publish paper. Most of the time full of bugs, doesn’t scale, don’t work across use cases, inconsistent results, slow, not supported, accuracy issues once you dig a bit deeper, catastrophic clinically wrong results in some cases.
You can’t get anyone to stand behind it in front of customer with issues.
Illumina at least build something proper of value they can stand behind. Others just copy open source and re-sell that junk.
There is certainly a sycophantic behavior around this software in the company. There are several high quality industry grade software out there. GATK et al. Accelerated calling on GPUs. One has to wonder what special value having wuch a bloated team buys Illumina? Yes the performance is slightly better in some cases but does one really care going from 99.9999 to 99.99999 accuracy? There are other ways to deal with stagglers.
Yet another waste from a company that is supposed to lead the way!
seems like an exciting release ...