Reviving an old thread. With the advent of the RTX nVIDIA GPU units, and the considerable efforts of nVIDIA to get people into GPU computing; we're very seriously considering buying a workstation with GPU capacity. Here are the current "Official" list of bioinformatics apps (https://www.nvidia.com/en-us/data-ce...tions/catalog/).
What are people's thought's on this new approach to GPU computing?
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So, last time this was discussed on SeqAnswers appears to have been mid-2016, and the answers were as I would expect:
http://seqanswers.com/forums/showthr...&highlight=GPU
After a lot of digging, I'm still not seeing any mainstream software tools designed for Bioinformatics workloads that utilize GPU's, though there is some work to improve distributed parallel computing functionality as in the case of "HipMer: An Extreme-Scale De Novo Genome Assembler" for example.
Just seems like the GPU architecture doesn't readily lend itself to the current algorithms and data sets perhaps?Leave a comment:
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GPU Enabled Bioinformatics Applications
In a bit of a debate with a colleague about how many (or, as I put it, how FEW) application codes are currently GPU-enabled in the wide application case considered "Bioinformatics". Of course, it probably depends on how broad one defines "Bioinformatics"...but when you look at the list of very commonly used applications that get regular coverage on SeqAnswers....I think VERY few are GPU capable.
So, how many broadly used Bio apps do YOU know of out there? Please feel free to name as well as comment on if the GPU "enhancement" is significant or not...
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Amplicon sequencing is a targeted approach that allows researchers to investigate specific regions of the genome. This technique is routinely used in applications such as variant identification, clinical research, and infectious disease surveillance. The amplicon sequencing process begins by designing primers that flank the regions of interest. The DNA sequences are then amplified through PCR (typically multiplex PCR) to produce amplicons complementary to the targets. RNA targets...03-21-2023, 01:49 PM -
Targeted sequencing is an effective way to sequence and analyze specific genomic regions of interest. This method enables researchers to focus their efforts on their desired targets, as opposed to other methods like whole genome sequencing that involve the sequencing of total DNA. Utilizing targeted sequencing is an attractive option for many researchers because it is often faster, more cost-effective, and only generates applicable data. While there are many approaches...03-10-2023, 05:31 AM
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