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SEQanswers.comSEQanswers is a discussion forum and information source for next generation sequencing. ForumsCopyright 2015 SEQanswers.comSEQanswers.com Posting/Responding on SeqAnswers Mon, 24 Aug 2015 19:45:41 +0000 If you are composing a new post (or creating a response to a pre-existing post) please make a copy of your text before you hit the "Submit/Post" button.

DDoS scans enabled on SeqAnswers may cause you to lose your post/text, if a scan is initiated just when you hit "submit". Having a copy of the text in clipboard will allow you to go back and recreate your post/response quickly and then post it successfully the second time (DDoS scans only happen after a set interval).
New Ion Torrent Sequencer? Thu, 06 Aug 2015 15:54:56 +0000 So I just read an article on talking about a new Ion Torrent based sequencer thats in the works. Apparently its called the S5 or S5 XL.

I tried looking for it online but couldn't find anything so I decided to ask here. Has anyone heard anything about this? Thanks!
Lotsa new toys from Illumina: HiSeq X Five, 3000, 4000, NextSeq 550 Mon, 12 Jan 2015 19:36:11 +0000 Hiseq 4000
Hiseq 3000
Nextseq 550
HiseqX 5
Site uptime issues, solutions. Fri, 27 Jun 2014 00:07:31 +0000 Hi all,

Wanted to post about the spotty service we've had the past few days and last week. Seems like we have been under some sort of sporadic attacks (from small network subranges) which spikes load making the site inaccessible.

If the site is down or responding very slowly, typically I will tweet from @SEQanswers, but as sequencing is a global activity, sometimes I'm asleep or in a meeting and don't tweet instantly.

With some help from my host and a security provider I hope I have addressed the issue in a robust way. If the site is down or slow, and I'm near my phone, I'll know about it.

Thanks for your patience.
ICGC-TCGA DREAM Somatic Mutation Calling Challenge Mon, 27 Jan 2014 14:15:38 +0000 Introducing the ICGC-TCGA DREAM Somatic Mutation Calling Challenge

We are very excited to announce an international effort to benchmark methods for identifying somatic mutations in cancer genomes from whole-genome sequencing. This message outlines the competition. We encourage all groups to download a set of standard datasets and submit their results. This will be useful to both algorithm-developers, to benchmark their newest techniques, and to data-analysts, to verify their current pipelines are internationally competitive! Details below, and registration at:

What problem are we trying to solve?

Cancer is a family of diseases caused by somatic genetic mutations. Fundamental questions remain about the causes of these mutations and their roles in shaping cellular phenotypes. The particular variations in tumour genomes can influence which treatments best suit patients. The genomics revolution is now systematically characterizing every somatic variation in every tumour for large cohorts (>300 patients). The bottleneck has now become the informatics analysis of these data. Accurately identifying these variants remains an open problem in the field. The major factor influencing the poor performance of today’s mutation callers is the heterogeneity of tumour biopsies. Cancer samples are a complex mixture of normal cells of different types and multiple tumour sub-clones, mixed together in ways that vary spatially within individual tumours. These sources of noise have profound effects on mutation callers. Benchmark studies conducted by TCGA and ICGC have discovered that different mutation calling software run on the same data have limited intersection between the resulting lists of mutations (overlaps of only ~20% are typical). Thus, a great debate has ensued about which software should be run to yield a unified set of calls for major cancer genomics efforts.

How are we trying to solve it?

In response, we have launched the ICGC-TCGA DREAM Somatic Mutation Calling (SMC) Challenge, a community-based collaborative competition of researchers from across the world, to find the most accurate SNV calling and break-point detection algorithms. This Challenge will create a “living benchmark” for mutation-detection pipelines, continually evaluating the best methods and accelerating the adoption of standards. evaluating the best methods and accelerating the adoption of standards. It will create a general platform extensible to addressing other key problems in cancer genome analysis, such as reconstructing tumour phylogeny, detecting fusion transcripts from RNA sequencing data, distinguishing driver from passenger mutations, amongst others.

How will the Challenge be run?
The Challenge will include two components. First, to help bring in researchers from other fields, a series of synthetic tumours of increasing difficulty will be simulated and made available to any team in the world, with a live leaderboard showing top results. Second, a set of 10 tumour-normal pairs from actual patients will be made available to any team, after approval of data-access by the ICGC Data Access Compliance Office. Importantly, methods will be evaluated in the real tumours by experimentally verification on the same patient DNA used for the original sequencing. Validation will be conducted for thousands (i.e., 5,000-10,000) of predictions via deep-sequencing using an independent technology, with the entire Challenge completed in about a year. Both somatic single-nucleotide and structural variation prediction accuracy will be benchmarked on both synthetic and patient-derived data, providing a global picture of mutation-detection accuracy.

The best performing methods will be applied retrospectively to over ten thousand cancer genomes, and the results distributed publicly to the research community via CGHub. Moreover, the top-scoring methods will be made available as an open source tools, allowing users around the world to process their own data using the same pipelines validated and used by the ICGC and TCGA. Challenge-assisted peer review and early editorial feedback will help identify publishable themes that cut across multiple approaches. The involvement of major journals introduces the possibility of reaching a broad audience and raises the impact and exposure of contestant contributions, which in turn increase incentives and overall morale. Nature Publishing Group has stepped up to coordinate publication models stemming from the SMC challenge.

What resources are available to Challenge participants?
The Challenge is run on the Synapse ( open computational platform. Synapse serves not just as a data repository but also as a set of tools for conducting collaborative analysis and sharing and documenting data, models and analysis methods. Synapse enables researchers to seamlessly and transparently conduct, track and share their ongoing work – building up living research projects in real-time.

GeneTorrent client, an open-source software developed by Annai Systems, is available for local data download. A comprehensive description of GeneTorrent features and operation is available on the CGHub website:

Google is offering Google Cloud Platform credits of $2,000 to approved DREAM contest participants, including free access to contest data in Google Cloud Storage. These credits can be used for Compute Engine VMs and other Cloud Platform services. Access to Challenge data is provided via a Google Cloud Storage bucket, so all computation and submissions can be performed on the Google Cloud Platform.

Who is running the Challenge?
  • Paul C. Boutros, Ontario Institute for Cancer Research
  • Lincoln D. Stein, Ontario Institute for Cancer Research
  • Josh Stuart, University of California, Santa Cruz
  • Gustavo Stolovitzky, IBM, DREAM
  • Stephen Friend, Sage Bionetworks
  • Adam Margolin, Sage Bionetworks
  • Thea Norman, Sage Bionetworks

The organizers include leaders of prominent national and international initiatives related to cancer-genome science. Leaders of the ICGC (Stein, Boutros) and TCGA (Stuart) cancer genomics projects will ensure broad exposure in the cancer genomics community and sanction that the results will set the standard for sequence analysis performed by the ICGC and TCGA. Challenge organizers also include leaders of DREAM Challenges (Stolovitzky, Friend, Margolin and Norman).

Where can I ask more questions?
We encourage all questions be posted on the ICGC-TCGA DREAM Mutation Calling Challenge Forum:
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 SEQanswers is online now at Bioinformatics.


(1) Avg response time to a new post in SEQanswers is less than 1 Day. Still decreasing !
(2) #Discussion & #Post per month keep rising !

SEQanswers: An open access community for collaboratively decoding genomes

We have more updated version of the figures, which is even more impressive. We plan to put them into SEQwiki
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.


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.


Technique/Chemistry: ?


Raw base accuracy 99.8%
100bp reads
~$99K for instrument?
$1K per run?


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 From In Sequence article

Hot damn!

ONT press release
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, 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 here, 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!

@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.