SEQanswers.com

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

Tue, 13 Nov 2012 20:20:43 +0000

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.

Oxford Nanopore @ ASHG

Wed, 07 Nov 2012 18:29:58 +0000

New thread started for ONT discussion as the old one was getting long. Also, GridION spotted in the wild? So it's not a hollow box... A call out to all ASHG attendees to please document ONT's announcements and hardware here for the community not attending.

SEQanswers published in Bioinformatics

Wed, 14 Mar 2012 11:40:05 +0000

Hi, We are excited to tell you the official publication for is online now at . Highlights: (1) Avg response time to a new post in SEQanswers is less than 1 Day. Still decreasing ! (2) #Discussion & #Post per month keep rising ! We have more updated version of the figures, which is even more impressive. We plan to put them into

New Tech at AGBT

Fri, 17 Feb 2012 10:28:09 +0000

I thought it might be useful to collate the bits and pieces about new platforms discussed during AGBT (Those that don't already have a thread), for those of us unlucky enough not to attended. Grabbing the info from various tweets listed at: If any one at AGBT could supply additional information from the talks, that'd be appreciated or any links to blogs covering the tech. GnuBIO Read Length: 1000bp Accuray: Phred 70+ Holopolymers: Phred 70+ to 9bp Sample Prep: < 1min System is rackable, ~30lbs, Dry Instrument fludics in cartridge. Beta Mid-2012, commercial end of 2012? Real time Variant calling, each base queried 6 times. Source: Technique/Chemistry: ? Website: LaserGen Raw base accuracy 99.8% 100bp reads ~$99K for instrument? $1K per run? Technique/Chemistry:? Website: So what do people think, do they sound interesting or is it all irrelevant and they'll be buried under ONTs upcoming announcement?

Oxford Nanopore to introduce "disruptive technology" at AGBT

Wed, 01 Feb 2012 16:04:19 +0000

Hot damn!

Roche hostile takeover bid for Illumina!

Wed, 25 Jan 2012 05:44:20 +0000

Roche is attempting a hostile takeover of Illumina...still absorbing this news...

Logo redesign contest underway, your help needed!

Thu, 19 Jan 2012 06:44:43 +0000

Hi all, I am holding a logo design content over at 99designs.com, and I would love some feedback from the community. The idea is to coordinate the (necessary) upgrade of vBulletin to 4.X with the deployment of a new logo and color scheme...but I want feedback from you all first! One can view all the designs submitted , or vote on my top choices by clicking on the image of the poll below. Please be brutally honest!

Illumina's newest upgrades (a response to Life Tech?)

Tue, 10 Jan 2012 17:23:14 +0000

For those of you who haven't been monitoring the latest thread over in the Ion Torrent forum. From Twitter: Illumina announces #HiSeq 2500: able to seq entire genome or 20 exomes in 24h. #JPM12 #GenomeInADay Illumina introduces #MiSeq enhanced performance w/ 3-fold throughput increase (7 Gb), faster cycles & 250 bp PE reads. #JPM12 How exciting! Edit: @illumina is working on new chemistry. "chemistry B" which is their stab at single molecule detection. #JPM12 I wonder if this has something to do with this:

Ion Torrent $1000 Genome!? Benchtop Ion Proton Sequencer

Tue, 10 Jan 2012 07:24:07 +0000

Does any one have any more information on this? Or had one in testing under an NDA and can now talk about it? Looking at the press release it seems they're claiming they'll have the whole Genome chip available near the end of the year. Looking at the images it looks like they're using a newer much larger chip. Does any one know what coverage they're talking about when they say a $1000 Genome, 1x, 10x or 30x?

The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis

Tue, 15 Nov 2011 17:45:17 +0000

Hi, We are excited to tell you that the paper for SEQanswers wiki (SEQwiki) is published today (15th Nov 2011) on Nucleic Acids Research Advance Access. Massive thanks go to all contributed to the content in SEQwiki. Dan, ECO, Krobinson, Mmartin, Andreas.sjodin, usad, Matthew Young, and marcowanger thank you all.

Let's make the SEQwiki even more awesome

Wed, 14 Sep 2011 19:51:40 +0000

Help make the Wiki awesome! The SEQanswers wiki (or "SEQwiki" for short) is a great help for users of this forum: It's a catalog of high-throughput sequencing tools. There is currently an effort to get the SEQanswers forum and the wiki published in the next NAR database issue. This is a to get the wiki in shape: Some of the tool descriptions are just "stubs", but in order for those pages to be really helpful, we need just . We invite everyone to pick one (or of course more!) tools that she or he uses and improve its description in the wiki. If you are the author of the tool, it is the best time to advertise there by writing to help people choose the tools. This will help others tremendously when they decide which tool to use. It's also the perfect opportunity to write down the sometimes things that are often not mentioned on the homepages of those tools. Here are some suggestions what you could write about your tool: Which tasks is the tool at? (something like: "really fast read mapping") What are the limitations? In which situations would the tool not be appropriate? ("cannot find indels", "needs at least least 32 GB RAM") Are there any ? Any idiosyncrasies when using the tool? ("be careful: if the input file is corrupt, there's no error message -- and the results will even look meaningful"). Hidden requirement? e.g. that said memory efficient but require 32GB or more for a reasonable small dataset? Which tools exist? ("if you still use MAQ, you should switch to BWA") Are there related tools? (on the BWA page: "Seal uses the BWA algorithm, but runs on a Hadoop cluster") Since the wiki is there to help us decide which tool to use for a specific purpose, please also try to . Just try to make it fit into the "Browse software" page! While you are editing and using the wiki, please also let us know about you have with the wiki software itself -- things perhaps only an administrator can change. Do any templates look ugly? Is the navigation too confusing? Don't like the fonts? We cannot promise to take care of everything, but ! Writing by M Martin. Thanks! The SeqWiki Publishing team want to thank you for the help

Lets publish the Wiki!

Mon, 01 Aug 2011 09:00:26 +0000

There is now a great opportunity to publish as a 'wiki-database' in the 2012 NAR annual database issue ! Below are 'the details' from the previous email exchange with the editors of NAR. I've started a preliminary page for collaborative authorship of the paper here: So lets get writing! (Sorry for the short notice, 14 days and counting!!!) Dan. --- Details... Dear Dan, Thank you for your interest in the 2012 Nucleic Acids Research database issue. Your proposal looks reasonable to me (don't know about the reviewers) and I am glad to invite submission of your paper. Please carefully read the instructions at the URL: Then go ahead and submit your manuscript by the August 15th deadline. Please let me know in advance if you need a delay of a week or so. Please note that we would ask you to include into your submission a supplementary file with a short description of your database in accordance with BioDBcore ( (see the examples at ) Best wishes, Michael Galperin On Fri, Jul 1, 2011 at 7:57 PM, Dan Bolser wrote: > Dear Michael, > > Please find below a pre-submission inquiry for the description of a > new wiki-database, SEQwiki (). > > > Sincerely, > Dan Bolser. > > SEQwiki : A Wiki Database for High-throughput Sequencing Tools and Technologies. > > Dan Bolser, Keith Robison, Andreas Sj�din, Marcel Martin and Eric Olivares. > > In recent years, dramatic advances in sequencing technology have > created unprecedented opportunities for biological discovery. At the > same time, however, this rapidly advancing and complex field has > created unprecedented challenges for data management and analysis. As > a consequence, the development of scientific software and > computational methods in the field is outpacing the speed of > peer-reviewed publication and other traditional forms of information > sharing. > > The SEQanswers forum () was founded to address > this gap; it facilitates the rapid dissemination of both wet-lab > techniques and information regarding computational tools and analysis. > The forum allows new tools, techniques and pipelines to be rapidly > announced, tested and benchmarked within the community. > > SEQwiki () is a Semantic MediWiki (SMW) site that is > edited and updated by the members of the SEQanswers community. The > wiki provides an extensive archive of categorized high-throughput > sequencing analysis tools, technologies and providers. > > Wiki pages provide structured data for each tool, including data types > and formats, capabilities, and provenance details as well as > catalogues of links to publications and online resources. Users > contribute both structured data and free text comments using a > combination of standard wiki and SMW data entry. A search tool > provides a simple means for finding information about particular > tools, and structured data can be queried and presented as reports > within the wiki. > > After two years, the SEQanswers community have created pages for over > 400 unique software tools, with around 350 references and 500 web > links. This effort has made the SEQwiki database the most > comprehensive and detailed archive of high-throughput sequencing tools > anywhere on the web. This community databases is an invaluable > resource for the high-throughput sequencing. -- -------------------------------------------- Michael Y. Galperin, PhD Executive Editor, NAR Database Issue E-mail: Phone: +1-301-435-5910 Fax: +1-301-435-7793 --------------------------------------------

Short Read Archive Canned

Mon, 14 Feb 2011 14:56:30 +0000

More details here: Where will you submit your data now?

2011 AGBT thread!

Tue, 01 Feb 2011 17:47:47 +0000

I'm sitting in the airport about to board a plane to Florida for and realized we didn't yet have a way to collect all the comments, live blogs, pics, etc that will undoubtedly start flowing in soon as the conference starts tomorrow afternoon! So consider this an open thread for all things AGBT related! I will also be posting to the @SEQanswers twitter account, with hashtags #AGBT and/or #AGBT2011, so you can stay in touch that way as well.

MiSeq

Wed, 12 Jan 2011 11:41:05 +0000

The latest addition to the Ilumina stable! What's next? Illumina have just released the instrument which allows a very quick turnaround on runs that may be useful for small genomes, QC runs of larger projects and personalised medicine. I could not see anything about reagents though and wonder if this is a single lane system or not. It is only going to image about 10% of a lane based on what we see in GAIIx or HiSeq. Of course the lane might only be 10% of the size of a HiSeq flowcell. There is also little about how it achieves such speed. The only thing they say in teh documentation is that new fluidics help speed things up, I am not sure how this makes an 8 fold difference though. 1 x 35bp 4 hours >120 Mb 2 x 100bp 19 hours >680 Mb 2 x 150bp 27 hours >1 Gb Who's first?