[Beowulf] Project Heron at the Sanger Institute [EXT]

[Tim Cutts]

Compute capacity is not generally the issue.  For this pipeline, we only need about 200 cores to keep up with each sequencer, so a couple of servers.   Genomics has not, historically, been a good fit for SETI at home style cycle-stealing, because the amount of compute you perform on a given unit of data is quite low.  A lot of genomics is already I/O bound even when the compute is right next to the data, so you don’t gain much by shipping it off to cycle-stealing desktops.

In fact, the direction most sequencing instrument suppliers are going is embedding the compute in the sequencer itself, at least for use cases where you don’t really need the sequence at all, you just need to know how it varies from a reference genome.  In such cases, it’s much more sensible to run the pipeline on or right next to the sequencer and just spit out the (very small) diffs.

Scientists are conservative folks though, they sometimes get a bit nervous at the thought of discarding the raw sequence data.

Tim

On 4 Feb 2021, at 10:27, Jonathan Aquilina <jaquilina at eagleeyet.net<mailto:jaquilina at eagleeyet.net>> wrote:

Would love to help you guys out in anyway i can in terms of hardware processing.

Have you guys thought of doing something like SETI at home and those projects to get idle compute power to help churn through the massive amounts of data?

Regards,
Jonathan
________________________________
From: Tim Cutts <tjrc at sanger.ac.uk<mailto:tjrc at sanger.ac.uk>>
Sent: 04 February 2021 11:26
To: Jonathan Aquilina <jaquilina at eagleeyet.net<mailto:jaquilina at eagleeyet.net>>
Cc: Beowulf <beowulf at beowulf.org<mailto:beowulf at beowulf.org>>
Subject: Re: [Beowulf] Project Heron at the Sanger Institute [EXT]



On 4 Feb 2021, at 10:14, Jonathan Aquilina via Beowulf <beowulf at beowulf.org<mailto:beowulf at beowulf.org>> wrote:

I am curious though to chunk out such large data is something like hadoop/HBase and the like of those platforms, are those whats being used?


It’s a combination of our home-grown sequencing pipeline which we use across the board, and then a specific COG-UK analysis of the genomes themselves.  This pipeline is common to all consortium members who are contributing sequence data.  It’s a Nextflow pipeline, and the code is here:

https://github.com/connor-lab/ncov2019-artic-nf [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_connor-2Dlab_ncov2019-2Dartic-2Dnf&d=DwMF-g&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=gSesY1AbeTURZwExR_OGFZlp9YUzrLWyYpGmwAw4Q50&m=jJhOeZORmye7vKliXyqrCd2Kvbe5xu9pHhLw4rNQmHM&s=lSbHd9Jxd4Dy9P7rosnrdgOmieVt-yzUuVI-MPK7TM0&e=>

Being nextflow, you can run it on anything for which nextflow has a backend scheduler.   It supports data from both Illumina and Oxford Nanopore sequencers.

Tim
-- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.




-- 
 The Wellcome Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.
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