100 Gb of Data per Day – Nextseq 500 Sequencing Services Now Available on Genohub

Nextseq 500, Genohub

Find Nextseq 500 service providers on Genohub.com

Access to the Nextseq 500, Illumina’s first high throughput desktop sequencing instrument, is now available on Genohub.com. While not the highest throughput instrument on the market, it is one of the fastest with up to a 6x increase in bases read per hour (compared to HiSeq). The instrument is ideally suited for those who need a moderate amount of sequencing data (more than a MiSeq run, less than HiSeq) in a short amount of time. We expect the highest interest to be centered around targeted sequencing (exome or custom regions) and fast RNA profiling. For exome studies, you can run between 1-12 samples in a single run and get back 4 Gb at 2 x75 or 5 Gb at a 2×100 read length. If you’re interested in RNA profiling at 10M reads per sample, you can multiplex between 12-36 samples together in a single run. A 1×75 cycle run takes as few as 11 hours to complete and 2×150 runs take ~29 hours.

You can order Nextseq 500 sequencing services today and expect to receive data back in 3-4 days ! Prices for 1 lane start at $2,250. Start your search here and use our helpful filters to narrow down your choices:  https://genohub.com/shop-by-next-gen-sequencing-technology/#query=e4c84df6f5ddd963cc48c30d3f93d505

After you’ve identified the service you need, communicate your questions directly to the service provider. We’ll make sure you get a fast response. Genohub also takes care of billing and invoicing, making domestic & international ordering a breeze. We also have an easy to use project management interface to keep communication and sample specification data in one place.

If you’re not familiar with Nextseq technology or how best this instrument can be applied to your samples, take advantage of our complementary consultation service: https://genohub.com/ngs-consultation/. We can help with your sequencing project design and make recommendation as to what sequencing service would be best suited for your experiment.

Last month we announced the availability of HiSeq X Ten services on Genohub: https://blog.genohub.com/the-1k-30x-whole-human-genome-is-now-available-for-1400/

As an efficient online market for NGS services, Genohub increases your access to the latest instrumentation and technology.  You don’t have to shell out $250K or $10M for a NextSeq or HiSeq X Ten, when access to professional services is right at your fingertips !

 

 

 

Yearly Demand for Whole Human Genome Sequencing – 400K New Genomes in 2015 ?

hgp_measures

(Figure courtesy of the National Human Genome Research Institute: http://www.genome.gov/27553526) 

Advances since the Human Genome Project ended in 2003 have been significant. With new Illumina sequencing instruments becoming operational in April, large facilities will be able to generate 18,000 whole human genomes (18,000 30x Genomes / HiSeq X Ten, a set of 10 HiSeq X Systems). As of today, these facilities include: the Broad Institute, Garvan Research Foundation, Macrogen, New York Genome Center, Novogene and WuXi PharmTech. At a rate of 1 genome / lane, this begs the question how many 30x human genomes will be sequenced in the next 3 years ? Let’s estimate that each facility will churn out around 25,000, 30x genomes/year (some of the facilities above have purchased multiple HiSeq X Tens, others have more than 10 daisy chained together). In 2015 yield from these facilities alone (assuming no one else purchased a machine) would be ~150,000 genomes. Optimistically doubling that to account for new HiSeq X Ten purchases between now and 2015 would give an estimate of ~300,000 genomes in 2015, and that’s only on the HiSeq X Ten. Assuming this year there will already be 60,000 30x (non-HiSeq X Ten) genomes sequenced, 20% growth brings this figure closer to ~400,000 genomes in 2015. While this figure certainly does not account for delays, instrument break downs, data analysis, storage and library prep bottlenecks, it represents optimistic potential for 2015.

The next question is who’s going to supply all the DNA ? Several new initiatives to sequence whole populations are quickly popping up. With £100m earmarked, the UK is planning on sequencing the genomes of up to 100,000 NHS patients by 2017 (instrument platform likely Illumina), Saudi Arabia also plans to map 100,000 of their citizens, with the Ion Proton in line ready to do all the heavy lifting: http://www.bbc.com/news/health-25216135. Craig Venter’s recent launch of the company Human Longevity plans to start sequencing 40,000 genomes with plans to “rapidly scale to 100,000 human genomes / year”: http://www.humanlongevity.com/human-longevity-inc-hli-launched-to-promote-healthy-aging-using-advances-in-genomics-and-stem-cell-therapies/.

Everything described above pertains to whole human genome sequencing and is not meant to undercut the significantly higher number of other species that will be sequenced between now and 2015. Our focus at Genohub is to make it easy for researchers interested in next generation sequencing services to access all the latest sequencing technology, including the HiSeq X Ten: https://genohub.com/shop-by-next-gen-sequencing-technology/#query=e304abac02105b87079fd1a19e70b9ed. Anyone can search for, find and order sequencing, library prep and analysis services, making owning an actual sequencing instrument not a requirement for getting access to good quality data.

 

 

The “$1K”, 30X Whole Human Genome is now available for $1,400

HiSeq X Ten Sequencing Services now Available on Genohub

You can now order whole human genome sequencing (~30x coverage) on Genohub.com for $1,400 / sample ($1,550 with library prep). The Kinghorn Centre for Clinical Genomics is accepting orders for their HiSeq X Ten service through Genohub.com.  In fact, you can order this service today: https://genohub.com/shop-by-next-gen-sequencing-technology/#query=5a4399a2a2cab432b240d2426c708472

Designed for population scale human genome sequencing, the HiSeq X Ten when operating individually can output between 1.6-1.8 Tb on a dual flow cell in less than 3 days (600 Gb / day). When running 10 in parallel, tens of thousands of genomes can be sequenced in a single year. While currently Illumina has limited the HiSeq X Ten to human samples, we expect this will change in 2015. 

A single lane of HiSeq X Ten, gives you 750M paired end 2x 150 reads, for a total output of 112.5 Gb / lane. Kinghorn guarantees 100 Gb raw data per lane, with >75% of bases above Q30 at 2x150bp. With a haploid human genome size of 3.2 Gb, that’s equivalent to 30-35x  per lane of sequencing.  The $10 million price tag for the HiSeq X Ten means that not all institutes have access to such sequencing power. Genohub solves this problem by making it easy for researchers interested in next generation sequencing services to access all the latest sequencing technology. We also:

  1. Ensure your project with the provider goes smoothly
  2. Take care of billing and invoicing, making domestic & international ordering a breeze
  3. Have an easy to use project management interface to keep communication and information in one place
  4. Offer NGS project design and consultation
  5. Have competitive pricing and turnaround times

Start your population study on Genohub.com today !

 

 

 

AGBT 2014 – Digest of Days 2 – 4

AGBT 2014 Summary

Days 2 – 4 of the Advances in Genome Biology and Technology meeting (AGBT) meeting were packed with great talks and insightful comments #AGBT14. For a summary of day 1 check out our earlier post. We’re just going to give a brief digest of the talks we attended and will update this blog post as we fill in more details.

Day 2 at the Advances in Genome Biology and Technology meeting (AGBT) started off with a cancellation of the much-anticipated talk by Evan Eichler on “Advances in Sequencing Technology Identify New Mutations, Genes and Pathways Related to Autism”. Dr. Eichler studies gene duplication and DNA transposition within the human genome. We’re assuming that what he was going to present was just published this month, “de novo convergence of autism genetics and molecular neuroscience”. Let us know if you know otherwise or when Dr. Eichler is speaking again!

Stephen Fodor, founder of Affymetrix announced a new approach for quantitation of mRNA transcripts in single cells. The method utilizes a single tube endpoint assay and allows for precise measurements of transcripts without the need for cycle to cycle real time measurements or physical partitioning (digital PCR). The procedure works by encoding all mRNA molecules with molecular barcodes allowing the user to amplify their samples and not worry about duplication rates. Pixel™, the name of their device is described in more detail in their white paper.

Hiroyuki Aburtani presented a lecture on applying epigenome profiling and single cell transcriptome analysis and demonstrated that Wnt / B-catenin signaling switches transcriptional networks and re-organizes the epigenome into specific pluripotent lineages. Their analysis is designed to improve the understanding of cell fate during differentiation.

David Jaffe’s much anticipated talk on the assembly of bacterial genomes using long nanopore reads generated a significant amount of interest. David presented data on two bacterial genomes, methylation negative E. coli and Scardovia. His conclusion was that the data was not useful by itself for de novo assembly, but he speculated on applications that would benefit from data where 84% of reads had at least a perfect 50-mer. This talk was nicely summarized by two other blog posts: The one and only Oxford Nanopore talk at AGBT 2014 – with real data and Oxford Nanopore Data and MinION: Valentines Day’s Gift to Genome Enthusiasts.

William McCombie’s talk demonstrated his group’s ability to generate 10 kilobase reads to assemble the Saccharoyces W303 genome using HGAP and the Celera Assembler. Their resulting contig N50 approached 1 million bases. Their hybrid assembly made it possible to generate whole genome, eukaryotic genomes that exceed BAC assemblies with Sanger sequencing.

Gene Myers discussed a new assembler called the “Dazzler” (the Dresden Azzembler) that can assemble 1-10 Gb genomes from PacBio RSII data. The advantages for the new assembler are that it can scale to Gb genomes 100 fold faster than current assemblers and it has a “scrubbing phase” that detects and corrects read artifacts that can cause problems with long contiguous assemblies. A nice summary of this talk is described in Dale Yuzuki’s blog post: http://www.yuzuki.org/favorite-talk-agbt-2014-gene-myers-max-planck-dresden/

 Hessam Esfandyarpour from Genapsys, presented on what they call a “truly cost-disruptive sequencing platform”, the GENIUS 110 System. Backed with just under $50 million in venture funds from Yuri Milner, DeChang Capital and IPV Capital, the GENIUS system uses nano-electronic technology (clonal amplification as opposed single molecule sequencing) combined with unmodified nucleotides and polymerase to generate “long reads”. They announced the Genius Club, an early access program, to test the instrument. While he did talk about consumables, three chips with 1Gb, 10Gb and 100Gb, he didn’t show much data. We’ll have to wait to hear more.

Jeffery Schloss, director of the division of Genome Sciences at the National Human Genome Research Institute gave a talk on “Ambitious Goals, Concerted Efforts, Conscientious Collaborations – 10 Years Hence”. His talk began with a graph measuring the cost per base on the y-axis and the years from 1990-2005 on the x-axis. He reiterated their strategic plan of Base pairs to Bedsides: http://www.genome.gov/Pages/About/Planning/2011NHGRIStrategicPlan.pdf. Schloss’s talk was nicely summarized in a recent Dale Yuzuki’s post.

We’re in the process of updating and adding summaries of talks from AGBT 2014. Check in again !

 

 

 

 

 

AGBT 2014 – Summary of Day 1

AGBT 2014 Summary

The first day of the Advances in Genome Biology & Technology (AGBT) meeting kicked off with an introduction by Eric Green, Director of the National Human Genome Research Institute. He announced that this 15th annual meeting was the largest ever with 850 expected to attend. The opening plenary session certainly did not look like 850 people in attendance. Winter Storm Pax wreaked havoc on flights coming in from Atlanta and other cities, resulting in several speaker and general attendee cancellations.

The plenary session began with scheduled talks by Aviv Regev, Jeanne Lawrence, Wendy Winckler and Valerie Schneider. Jeanne Lawrence couldn’t make it, which was a shame particularly since she gave a brilliant talk at ASHG on using a single gene XIST to shut down the extra copy of chromosome 21 in Down syndrome. This work was nicely summarized in a publication that came out this summer titled: Translating dosage compensation to trisomy 21.          

Aviv Regev and Wendy Winckler’s talks were subject to a blog/tweet embargo (unclear whether Regev’s talk was completely under embargo or only the last half, we’re playing it safe and not discussing it here), leaving Valerie Schneider’s presentation the only one that was tweeted or written about. This instantly created great angst among those attending the lectures, those stuck in airports enroute to AGBT and those at home waiting for in depth coverage.

Single-cell sequencing, considered the “method of the year” by Nature Methods was the basis of the opening lecture. Aviv Regev offered an excellent view of the dendritic cell network based on cyclical perturbations and variations between single cells. Regev’s first half of her presentation titled, “Harnessing Variation Between Single Cells to Decipher Intra and Intercellular Circuits in Immune Cells” was largely covered by her publication in April, “Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells”.

The second talk, by Wendy Winckler was not allowed to be discussed or tweeted according to Winckler, courtesy of Novartis’s communications department. The title of her presentation “Next Generation Diagnostics for Precision Cancer Medicine” wasn’t revealing either. To get an idea of what she’s up to and the direction of her lecture, you can read these recent publications.

The final talk by Valerie Schneider, titled “Taking advantage of GRCh38” began with an analogy to an unwanted pair of socks one receives for Christmas that ends up being used and finally really liked. “It was time for an update….whether or not it was on your wish list”. We were reminded that centromeres are important specialized chromatin structures important for cell division, but because of repetitive regions, they are not represented in reference assemblies. Previous versions of the human reference assembly had centromeres represented by a 3M gap. The latest assembly, GRCh38 incorporates centromere models generated using whole genome shotgun reads as part of the Venter sequencing project. Since there are two copies of each centromere for each autosome, these centromere models represent an average of two copies. She concluded her presentation urging users to switch now: http://www.ncbi.nlm.nih.gov/genome/tools/remap.

 After a short break from the talks, the closing reception sponsored by Roche began outside. Halfway through, there was a brief yet sudden Florida thundershower that sent the entire AGBT community scurrying indoors for shelter. That was okay though because the conversations just continued indoors. Looking forward to tomorrow morning’s lectures. Several of the ones we’ve highlighted will be up.

 

2014 AGBT Agenda Highlights

AGBT 2014 Agenda

The yearly genomics pilgrimage to Marco Island begins next Wednesday from Feb. 12th until the 15th. The 15th Advances in Genome Biology and Technology (AGBT 2014) Agenda was released last week, it’s guaranteed not to disappoint. We expect the following lectures to be the most interesting: 

Aviv Regev, Broad Institute of MIT and Harvard
“Harnessing Variation Between Single Cells to Decipher Intra and Intercellular Circuits in Immune Cells”

-Single cell genomics is becoming an extremely useful tool, we’re eager to hear more on the first day of the meeting. 

Jeanne Lawrence, University of Massachusetts Medical School
“Silencing Trisomy 21 for Genome Balance in Down Syndrome Stem Cells”

– Her talk was the most tweeted plenary lecture during ASHG 2013 and it was great! A must go!

Evan Eichler, University of Washington
“Advances in Sequencing Technology Identify New Mutations, Genes and Pathways Related to Autism”

– Dr. Eichler studies gene duplication and DNA transposition within the human genome. This is going to be a good talk.

Beth Shapiro, University of California, Santa Cruz
“Paleogenomes, Ice-age Megafauna, and Rapid Warming: How Genomes From the Past Can Help Predict the Consequences of the Future Climate Change”

 – The paleogenomics section of the recent PAG conference was excellent. I expect this to be an interesting lecture as well. 

 Andrea Kohn, University of Florida
“Single-Neuron Semiconductor RNA-seq with Nanofluidic Capture: Toward Genomic Dissection of the Complex Brains and Memory Circuits”

– Lots of good RNA-Seq talks. Dr. Kohn’s single cell sequencing approach is described here: Single-neuron transcriptome and methylome sequencing for epigenomic analysis of aging  and here: Single-cell semiconductor sequencing.

Stephen Fodor, Cellular Research, Inc.
“Digital Encoding of Cellular mRNAs Enables Precise and Absolute Gene Expression Analysis by Single-Molecule Counting”

– What’s next from the founder of Affymetrix? For a preview check out their paper that came out this month on molecular indexing for quantitative targeted RNA-Seq.

 James Hadfield, Cancer Research, UK
“Monitoring Cancer Genome Evolution with Circulating Tumour DNA Exome Sequencing”

– Looks interesting. Hoping to get a preview from his blog: CoreGenomics

Hiroyuki Aburatani, The University of Tokyo
“Single Cell RNA Sequencing Reveals Transition of Cell Populations with Epigenomic Switch in Cell Fate Determination Along Cardiomyocyte Differentiation”

Brian Haas, Broad Institute of MIT and Harvard
“Single Cell Developmental Genomics: Trinity-Enabled Single Cell Transcriptome Study Identifies New Regulators of Salamander Limb Regeneration”

 David Jaffe, Broad Institute of MIT and Harvard
“Assembly of Bacterial Genomes Using Long Nanopore Reads”

– Expecting to see some of the first Nanopore data here !

W.R. McCombie, Cold Spring Harbor Laboratory
“A Near Perfect de novo Assembly of a Eukaryotic Genome Using Sequence Reads of Greater than 10 Kilobases Generated by the Pacific Biosciences RS II”

Hesaam Esfandyarpour, Genapsys, Inc.
“The GENIUS™ Platform: A Next Generation Sequencing Platform That Exceeds Quality and Cost Goals for Universal Deployment In and Out of Core Laboratory Environments”

– The latest NGS platform, Genapsys just got $37M in series B financing

 Zak Wescoe, University of California, Santa Cruz
“Error Rates for Nanopore Discrimination Among Cytosine and Four Epigenetic Variants Along Individual DNA Strands”

Yaniv Erlich, Whitehead Institute for Biomedical Research
“Genome-Wide Analysis of Expression Short Tandem Repeats”

Carlos Bustamante, Stanford University
“Any Way You Want It: Applications of Whole Genome Capture to Ancient DNA, Metagenomics, and Orthogonal Validation”

Daniel MacArthur, Massachusetts General Hospital
“Functional Annotation at Scale:  Analysis of Genetic Variation From Over 50,000 Human Exomes”

Genohub will be in attendance and tweeting @Genohub. Send us a message and let’s meetup to talk NGS !

Matchmaking for the Life Scientist

Seq-ing NGS data analyst for long walks on the beach (Marco Island). Experience with SNP calling and genome mapping a plus. Must be willing to deal with large data sets and my species diversity. Willing to pay hourly for a short term (one-time) relationship. Also offering to include you as an author on my paper. 

So maybe you haven’t seen a request exactly like this one, Genohub has ! There are typically two main types of people using Genohub.com.

There is the researcher who is completely new to next-gen sequencing. He or she may know nothing about sequencing read types or how to analyze data and needs help starting. The researcher may have some resources, but needs help with sequencing and / or  data analysis.  These researchers can begin their foray into NGS using our complimentary consultation form. This researcher will talk with our scientific staff and get matched with a sequencing service provider or bioinformatician best suited to handle their project. 

 Then there’s the experienced NGS researcher who has ordered library prep, sequencing or data analysis services before and knows exactly what he or she wants. Often this researcher needs to discuss a few things with a service provider before moving things forward. This type of researcher can find service providers based on the NGS instrument or library prep application they need using Genohub’s technology search page or enter the number of reads / coverage they need using our project specific search engine. Using either search applications, the researcher can find, submit their project and talk directly with a service provider.

So the next time you’re ‘seqing’ a match for your next-gen sequencing project, start with Genohub.com.

next generation sequencing consultation

 

Consider Bias in NGS Library Preparation

Library preparation for next-generation sequencing involves a coordinated series of enzymatic reactions to produce a random, representative collection of adapter modified DNA fragments within a specific range of fragment sizes. The success of next-generation sequencing is contingent on this proper processing of DNA or RNA sample. However as you go from isolating nucleic acid to finally interpreting your sequencing data, assumptions and bias prone steps can quickly reduce the value of your work. This is especially the case during library preparation.

Where are biases introduced ?

The first step in most library preparation is shearing of your DNA or RNA to fragments that are compatible with today’s short read NGS instruments. Whether you fragment your nucleic acid material using a high divalent cation buffer, nuclease, transposase, acoustic or mechanical method, you are invariably cutting at “preferred” positions resulting in fragments with non-random ends. In DNA-Seq/ChIP-Seq library prep procedures the next step is to end-repair or repair 5’overhangs and fill in 3’overhangs using a couple polymerases (or fragments of a polymerase). If you’re starting with variably fragmented ends, this process isn’t going to occur at the same efficiency for all your fragments, and neither will adenylation of these ends (commonly performed after end-repair). The next step is typically ligation of an adapter that is compatible with the instrument you plan to use. Unfortunately there aren’t that many studies that have examined bias in DNA adapter ligation. However, if you’re keeping up to date with papers coming out on RNA adapter ligation bias, there is reason to be concerned. To complete your library you typically have to amplify it, which can lead to preferences for particular fragments, and un-even fragment representation in your data. We’re just talking polymerase bias in PCR here, we haven’t even mentioned the polymerase biases on board the sequencing platform.

All RNA-Seq library prep procedures utilize reverse transcriptases that often have issues reading through regions of RNA that have secondary structure or specific base compositions. The reverse transcriptase primer you choose can also bias your results. Follow that with second strand synthesis and all the steps described above for DNA-Seq and you now have potentially the most compromised library application on hand.

A recent review nicely highlights some of these biases in more detail: Library preparation methods for next-generation sequencing: Tone down the bias

It’s not all doom and gloom, there are several ways you can reduce or measure these biases.  For example using randomized bases in small RNA library preparations, eliminating PCR  or even using a polymerase that can handle GC / AT rich regions fairly equally. Eliminating or reducing these biases will be the subject of a subsequent blog post.

Consistency in library prep method

For many applications, as long as all your samples are being treated equally, biases introduced during library preparation affect all your samples and may be less of a concern. If you’re in the middle of a long project, we highly recommend using the same library prep method or kit for your whole study. Differences in method, enzymes and reaction times between two different library prep kits can give you significantly different results. To understand differences in library preparation methodology, we have a NGS Library Prep Kit Guide that describes kits providers use on Genohub.

If you’d like help navigating issues in library preparation bias or would like to use our complementary consultation service, contact us !

 

NextSeq 500 and HiSeq X Ten: New Tech Lowering Cost per Mbp

Jay Flatley’s announcement yesterday certainly changes calculations for whole genome sequencing. Newer, cheaper optics, fluidics and reagent chemistry have lowered the cost of sequencing and enabled a 300 cycle, 125 Gb run in 30 hours with the NextSeq 500. The HiSeq X Ten, (pronounced ex ten, not ten ten) consisting of 10 instruments daisy chained together, will generate 18 Tb in 72 hours.  The new optical technology now utilizes a 2 dye system: adenine and cytosine bases are represented by one dye, an absence of dye for guanine bases and both dyes for thymine. This allows Illumina to utilize lower resolution cameras with half the number of images. The new patterned flow cells with larger clusters use nano wells and are scanned bi-directionally making optical scanning 6 times faster than a HiSeq 2500. New reagent chemistry now allows reactions to occur at room temperature, eliminating the need for a bulky chiller which reduces the instrument’s size to that of a Miseq, leading to the commonly quoted phrase: “HiSeq in a MiSeq”.

What’s the cost ?

The NEXTSeq 500 will cost $250,000 and the HiSeq X Ten must be purchased in sets of 10 at $10 million for a full set. According to Illumina, the HiSeq X Ten will yield whole human genome sequences for $1,000 each and will have the capability to generate around 15,000-20,000 genomes per year. The NEXTSeq 500 will be able to generate 120 Gb or 4, whole human genomes at 30x coverage for ~$4,000.

Excess capacity

So what will providers be doing with all this excess capacity….enter Genohub.com.  Genohub’s intelligent sequencing matching engine instantly matches researchers with service providers based on specific project criteria. Genohub facilitates the management of sequencing projects throughout the sequencing lifecycle from selecting orderable sequencing packages, to communication, payments and delivery of data. In March, NGS service facilities are going to need to recoup operational costs and convince their institutions they made the right choice dropping $250K for a NEXTSeq 500 or $10M for a HiSeq X 10 cluster. We estimate that toward the middle of 2014 there will be a lot of available NEXTSeq 500 flow cells needing filling and a much higher number of whole human genomes needed for the HiSeq X 10. Regulatory issues, data analysis bottlenecks and operational logistics will most likely keep the 5 HiSeq X 10’s fairly quiet in 2014 (Illumina has promised 5 in 2014, 3 have already been purchased). Genohub is uniquely positioned to distribute this excess capacity to researchers around the world.  Your local institution or even country no longer need to have one of these instruments on hand (See our post on reasons to outsource NGS services). By using Genohub.com, you have access to sequencing capacity and instruments located throughout the world.

Looking to use the NEXTSeq 500 ? After discussions with our current service providers, we expect NEXTSeq 500 sequencing services to be available on Genohub in 3 months. We’ve already spoken to one of the announced HiSeq X 10 customers and hope to have that service available on Genohub shortly after delivery.  So today, we’re happy to announce that Genohub is taking NEXTSeq 500 pre-delivery service requests ! Send your request through our consultation form. Check back with us in March for regular access to these platforms using our intelligent sequencing search engine.   

HiSeqX_Ten_Image

 

 

Top Next Generation Sequencing Applications

A common question we’re asked is what library preparation applications are researchers most interested in. Providers starting their own core facility, bioinformaticians writing software for a particular pipeline and others trying to gauge demand for NGS applications are most interested in this answer. In the last three months we looked at the number of initiated projects on Genohub that included library preparation. Projects initiated on Genohub are made through our Shop by Project: https://genohub.com/shop-by-next-gen-sequencing-project/ or our Shop by Technology: https://genohub.com/shop-by-next-gen-sequencing-technology/ interfaces. Users enter project information like coverage or the number of required reads and can specify if they prefer one platform over another. Genohub’s intelligent project matching engine takes this data and displays packages that consist of provider services that match the user’s request. Users who select a package and begin direct communication with the provider are considered those who have initiated a project. A summary of the library preparation applications those users choose in the projects started between 10/2013 and 12/2013 are plotted in Figure 1 (data of projects using our complementary consultation service was also included in this graph).  

projects started

RNA-Seq projects encompass all those starting with Total RNA, ribosomal depleted and poly-A select RNA. These applications were the most popular followed by projects involving whole genome sequencing. RNA-Seq’s growing versatility as both an expression analysis and de novo assembly/construction tool are likely the reasons for the greatest number of projects on Genohub. Targeted DNA applications were also frequently performed as Exome, 16S V4 and other Amplicon-Seq projects consisted of the 3rd, 4th and 5th most commonly started projects on Genohub. While not illustrated in Figure 1, specialized applications related to Methyl-Seq and ChIP-Seq were some of the fastest growing.

Having recently started, we expect these numbers to grow significantly. We’ll keep the community updated with our latest data. If you’re a researcher or service provider that has a unique NGS application, we’d like to hear about it ! For inquiries or suggestions please contact us at support@genohub.com.