3 ms·

Analysis is custom if you are doing genomics right at this time. Either you are doing something pre-clinical, and you better understand what you are doing i.e.

by jerven 11y ago

Analysis is custom if you are doing genomics right at this time. Either you are doing something pre-clinical, and you better understand what you are doing i.e. analysis in a black box is not ok. Or you are not dealing with human stuff at all and then there is no analysis in a box on the market. There are tools with GUI's but they don't help that much if you don't understand the underlying systems.

adenadel 11y ago
I don't agree with you. I would argue that Genomics England is doing genomics right with the 100k genomes project and they certainly aren't doing custom analysis. Their pipeline is standard through variant calling and annotation. The WGS pipelines are pretty well established at this time. What you do with your VCFs is what can be customized. There is no reason for a small lab to write their own aligner or variant caller. The most that many do is write wrappers to create "customized pipelines", which is really just reinventing the wheel. EDIT: I want to clarify my mindset. In the environment that I work in there are three stages of analysis: primary, secondary, and tertiary. We mostly ignore the tertiary stage (I'm not actually doing science). Primary analysis is on instrument (base calling), secondary analysis takes you through variant calls and annotation, and tertiary analysis is where the real science happens. When I'm talking about canned analyses I'm talking about what I refer to as secondary analysis. Tertiary analysis is a very hard problem and will often require custom solutions. In my mind I'm separating bioinformatic analysis (secondary analysis) with interpretation (tertiary analysis).
- jerven 11y ago
  Getting the variants out is where the analysis starts. What does the variation mean, which ones correlate with a detectable phenotype. Which ones are affecting regulatory systems. Genomics England is brilliant because it has good access to excellent NHS data which it will use to do a lot of analysis. Which its not getting off the shelf but a lot of talented clincal+bio+informaticians are working hard on that. Or in other words getting the variants to the human genome reference is just the start of the analysis not the end. i.e. I am more worried about the end of the pipeline than the contents of them. I suspected as much on the 1,2,3 level. But even 2 is not really fixed yet. There are great off the shelf tools but even the concept of variation calling against a reference linear genome is not perfect yet especially with the alt_loci business. Which driving the variation graph work in the GA4GH projects.
- jeserac 11y ago
  It's not strictly true that we're not doing custom analysis. It must also be understood that while Genomics England have some standard pipelines running we are also providing the capability for partners via our GeCIP programme to work within a walled garden to do custom analysis within domains for rare diseases and cancers. You can read more about that here: http://www.genomicsengland.co.uk/about-gecip/ http://www.genomicsengland.co.uk/about-gecip/

by jerven 11y ago

adenadel 11y ago

I don't agree with you. I would argue that Genomics England is doing genomics right with the 100k genomes project and they certainly aren't doing custom analysis. Their pipeline is standard through variant calling and annotation. The WGS pipelines are pretty well established at this time. What you do with your VCFs is what can be customized. There is no reason for a small lab to write their own aligner or variant caller. The most that many do is write wrappers to create "customized pipelines", which is really just reinventing the wheel. EDIT: I want to clarify my mindset. In the environment that I work in there are three stages of analysis: primary, secondary, and tertiary. We mostly ignore the tertiary stage (I'm not actually doing science). Primary analysis is on instrument (base calling), secondary analysis takes you through variant calls and annotation, and tertiary analysis is where the real science happens. When I'm talking about canned analyses I'm talking about what I refer to as secondary analysis. Tertiary analysis is a very hard problem and will often require custom solutions. In my mind I'm separating bioinformatic analysis (secondary analysis) with interpretation (tertiary analysis).

jerven 11y ago
Getting the variants out is where the analysis starts. What does the variation mean, which ones correlate with a detectable phenotype. Which ones are affecting regulatory systems. Genomics England is brilliant because it has good access to excellent NHS data which it will use to do a lot of analysis. Which its not getting off the shelf but a lot of talented clincal+bio+informaticians are working hard on that. Or in other words getting the variants to the human genome reference is just the start of the analysis not the end. i.e. I am more worried about the end of the pipeline than the contents of them. I suspected as much on the 1,2,3 level. But even 2 is not really fixed yet. There are great off the shelf tools but even the concept of variation calling against a reference linear genome is not perfect yet especially with the alt_loci business. Which driving the variation graph work in the GA4GH projects.
jeserac 11y ago
It's not strictly true that we're not doing custom analysis. It must also be understood that while Genomics England have some standard pipelines running we are also providing the capability for partners via our GeCIP programme to work within a walled garden to do custom analysis within domains for rare diseases and cancers. You can read more about that here: http://www.genomicsengland.co.uk/about-gecip/ http://www.genomicsengland.co.uk/about-gecip/