SEQanswers.com

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?

Assemblathon: Collaborative Assembler Comparison!

Tue, 11 Jan 2011 16:50:06 +0000

The folks at the UCDavis Genome Center are organizing a collaborative effort to evaluate and improve genome assemblies. This looks like it will be very informative in determining which assemblers perform well on what data types. Find the Assemblathon here: Thanks to Nickloman for bringing this to my attention.

In Sequence conducting NGS Survey

Thu, 09 Dec 2010 15:36:51 +0000

In Sequence is conducting an anonymous survey of next gen sequencing users, and Julia Karow asked me to post the link here: Please participate if you are interested, In Sequence is free for academic/non-profit users.

Free NGS Sample Prep Symposium Dec 15, Bay Area

Wed, 08 Dec 2010 19:50:24 +0000

"AUTOMATING THE NEXT GENERATION SEQUENCING WORKFLOW" Hosted by LRIG Bay Area Date and Time: December 15, 2010, 12:00 PM to 6:00 PM Location: South San Francisco Conference Center Free Registration: We will investigate the latest methods and technologies to fully exploit Next Generation Sequencing, including upstream library preparation and template amplification. Clinical applications for emulsion PCR will also be explored. The event is free, a buffet lunch is served at 12:30 prior to the presentations. There will be twenty vendors serving the genomics community exhibiting. Confirmed Speakers: Emily Leproust, Ph.D., Agilent Technologies, Director Applications and Chemistry R&D - Genomics The Agilent Technologies SureSelect(tm) Platform for Target Enrichment William Donahue, Ph.D., Manager, Molecular Biology, Beckman Coulter Genomics SPRIworks - An Automated Sample Preparation System for Second Generation Sequencing Platforms Take Ogawa, Raindance Technologies Finding Needles in the Genomic Haystack: targeted sequencing for rare variant analysis Serge Saxonov, Ph.D., VP, Applications Development, Quantalife A novel droplet digital PCR platform accurately detects and quantifies molecular targets exceeding performance of other methods by orders of magnitude

SEQanswers/SEQwiki AGBT poster abstract?

Tue, 09 Nov 2010 21:14:48 +0000

ECO came up with the plan of submitting a SEQanswers / SEQwiki poster to AGBT 2011 (The 12th annual Advances in Genome Biology and Technology): The current draft abstract is here, and I'd welcome any input (the deadline is Friday!): I thought it would be cool to acknowledge all the wiki contributors in the author list of the poster. As hundreds of authors is a bit of a logistical pain, I've just listed the top 20 contributors. Let me know what you think!

1000 Genomes paper out today in Nature

Thu, 28 Oct 2010 10:13:25 +0000

Many here will have this in word in a pre-submission format... for the rest of us, here it is: