Comments on: Next-Generation Sequencing Informatics Update

By: snet

snet — Mon, 01 Mar 2010 05:01:08 +0000

yeah.SOLiD v3 plus spec sheet will have all those numbers you need.

http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_072050.pdf

By: dd

dd — Sat, 20 Feb 2010 22:06:05 +0000

Keith, I get production numbers on the platform we do not have (SOLiD), from drd at Baylor.

Alejandro, I saw that you updated your post, and I appreciate it. I did not mention it in this post to impugn you, rather to help make a point.

Dirk, it’s true that mate-pair and paired-end are different, but for the purposes of this table the distinction is not important (indeed, it can easily be inferred by the size of the insert). None of the submission data is for images. It is for SRF (now ~17 B/b but ~50 B/b at one time) or gzipped FASTQ (~0.1 B/b). When the SRA has a fully functioning BAM pipeline, I have those numbers (~1 B/b). Note that I leave the SRF for the older platforms for historical reasons. As for SOLiD 3+, I am happy to post them if someone can provide them (see above).

By: Dirk

Dirk — Sat, 20 Feb 2010 09:16:02 +0000

Mate-pair and paired-end should not be confused as they are fundamentally different chemistries. Also, the SRA does not require the submission of images and so most submitters are not uploading images. Is this removed from the SRA file size (it seems quite high given our experience).

Finally, some statistics for the SOLiD 3+ would be great as they are regularly producing 800M-1B 50+50 reads per run (2 slides).

By: Alejandro Gutierrez

Alejandro Gutierrez — Sat, 20 Feb 2010 05:51:27 +0000

Thanks for the update and clarification. I’ve corrected “somewhat dated” on our blog with a more faithful explanation.

By: Keith Robison

Keith Robison — Sat, 20 Feb 2010 02:36:24 +0000

I’m curious what you use for your source of statistics for platforms you don’t have direct access to — publications or you have a good network of other labs?

This is very useful information!

By: James

James — Sat, 20 Feb 2010 01:55:19 +0000

Thanks for the update, that table is a great resource whenever we start doing back of the envelop calculations for potential new projects.