SEQstandards and MINSEQE: Minimum Information about a high-throughput SeQuencing Expt

[Joann]

Introduction to the forum: a new standards page at the SEQWiki.

Our new Wiki page hopes to be a quick and easy source of standards guidance from FGED-MINSEQE as well as various other global standards initiatives relevant to forum members with the idea of helping to put things out there sooner than later. The FGED board has chosen SEQanswers as the most appropriate location in the entire webverse to host feedback opportunities on their consensus format for ultra high through put sequencing experiments. The forum is a great place to conduct discussions, and already has been active in exploring terminology issues and more. This thread would be a place to start collecting these discussions, plus feedback, inquiries and input from our forum members and also to refer students, especially, to the new Wiki page material on formal standards guidelines for sequencing and publishing sequence data.

[marcowanger]

The SEQwiki page: http://seqanswers.com/wiki/Standard

The MINSEQE page by FGED: http://www.mged.org/minseqe/

[marcowanger]

One question, I am not sure about the Minimum information about array. How was that minimal information about microarray expression got accepted as the standard for publication? What was the turning point?

[Joann]

See the 2nd page, 2nd paragraph of the article "Minimal information about a microarray experiment (MIAME)..."

http://www.frontiers-in-genetics.org/documents/gen-services/miame_standards.pdf

[marcowanger]

Thanks Joann

See the 2nd page, 2nd paragraph of the article "Minimal information about a microarray experiment (MIAME)..."

http://www.frontiers-in-genetics.org..._standards.pdf

[Joann]

Role of SeqAnswers and the pipeline in cancer research

I am posting here a link to informative slides from a recent talk given by Francis Ouellette, Ontario Institute for Cancer Research which he presented at the October 22, 2012 meeting of FGED in Toronto. Slide 20 includes a statement acknowledging the critical role of open access resources and SEQanswers (see slide 20)

https://dl.dropbox.com/u/7854957/Ouellette_ICGC_Toronto_Oct2012_FGED_ver02.pptx

[adaptivegenome]

I would love to know this fits or does not fit within standards for NGS, but we recently unveiled a new online tool with datasets, metrics, and comparison of major NGS pipeline tools. The whole project is crowdsourced and all datasets and results are free for use by anyone:

https://www.bioplanet.com/gcat

One application I think is for example when people discuss mapper comparisons on SEQanswers (as we have seen many times in the past), we can now link to comparisons that are not static images but interactive charts and anyways I think this can help us all get on the same page.

The project is brand new and there is lots to add, but I would love to gauge interest. I will write up a proper post on SEQanswers in a new thread sometime soon.

[Joann]

Yes

Yes, I would recommend writing these things up in some detail, vetting it here on the SEQanswers forum for any additional comment or question by users, either in synopsis form or as a link to the entire protocol or both, and then consider making it a formal presentation to the FGED board for possible adoption and/or a presentation at the next FGED meeting and also posting it to the Wiki site.

[marcowanger]

Joann,

It would be good if we can do so!

AdaptiveGenome,

I think the GCAT would be very useful, not only on evaluating pipelines in a more interactive way. At certain time point, would you think GCAT would also act as a portal for proficiency test platform for clinical NGS lab?

I think what the clinical NGS field lack so far (in a public scale) is that one that

1) provide reliable CRM
2) provide an independent platform to assess the result.

Regards,
Marco

Yes, I would recommend writing these things up in some detail, vetting it here on the SEQanswers forum for any additional comment or question by users, either in synopsis form or as a link to the entire protocol or both, and then consider making it a formal presentation to the FGED board for possible adoption and/or a presentation at the next FGED meeting and also posting it to the Wiki site.