[ensembl-dev] Performance Analysis and Hardware Acceleration of VEP.

[Syed Hossain]

Hello Muhammad Ali Akhtar,

Thanks for the query!

1. So we do have our performance analysis on VEP which was published on 
the latest paper. You can check the result here -
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0974-4.

2. VEP have option to run in multiple thread (--fork option, see - 
https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_fork) 
which suitable to run on multiple core clusters. And some of the 
underlying computation (such as linkage disequilibrium stats) are in C 
and Perl works as a wrapper. We do have a longer time plan to switch to 
a modern language.

Hope that answers your query.

Best regards,
Nakib

On 2022-08-27 14:20, Muhammad Ali Akhtar wrote:
> Hello Everyone,
> 
> This is my first time interacting with the VEP dev team. Just had a
> few questions.
> 
> 1. Are there any studies / reports out there with runtime /
> performance analysis of VEP?
> 2. Have there been any efforts on improving VEP performance? like
> coding in different languages (C/C++/) or using different processors
> (GPUs / FPGAs)?
> 
> I ask this because many steps (Like sequence alignment, variant
> calling)  in the genome processing pipeline are being targeted for
> hardware acceleration but I couldn't find anything on customising /
> improving VEP run time. Is it because the runtime of VEP has been
> short / average even for most demanding workloads?
> 
> Regards,
> Muhammad Ali Akhtar
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog: http://www.ensembl.info/