Xomics brochure 2013


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This is the Xomics NGS data analysis bioinformatics package, now available from AZCO.

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Xomics brochure 2013

  1. 1. Xomics™ Integrated Solution for Personal BioInformatics©Copyright 2013, Azco Biotech, Inc., San Diego, CA
  2. 2. XOMICS™ Page #: 2 Call us at +1-858-259-9528 or visit www.azcobiotech.com
  3. 3. XOMICS™Welcome to Azco Biotech, Inc.Azco Biotech, Inc. is the premier supplier of solutions for nucleic acid synthesis and sequencedetection.Azco’s products include solutions for genome sequencing, capillary sequencing, real-time PCR,PCR instruments and DNA and RNA synthesizers. We provide for each of these products acomprehensive set of reagents and backup all of the products that we sell with world-classservice.For DNA and RNA synthesis; Azco provides the complete solution from start to finish. Azcooffers a variety of instruments options from low throughput bench top models to high volumeproduction systems and we back all of our instruments with “world class” service In addition,Azco is your one source for high quality reagents including; supports, Phosphoramidites,modification reagents, labeling reagents and products for oligonucleotide purification.For Sequencing; Azco provides the complete solution from start to finish. Azco offers a varietyof instruments options and we back all of our instruments with “world class” service Inaddition, Azco is your one source for high quality reagents including; library and sequencingkits for 2nd generation sequencing as well as polymer, buffer, CARE solution and otherreagents for 1st generation sequencing. Azco also provides turn-key solutions forbioinformatics.All of our reagents are manufactured using cutting edge production processes that adhere tostringent quality control. Our reagents are thoroughly tested to assure they meet the highestpossible quality standards and then packaged in the right bottles for your synthesizer.Customers rely on us to deliver quality, so that’s what we deliver!To ensure that our products exceed the highest levels of quality, they are manufactured understrict quality systems. Since they are produced to meet such stringent quality requirements theyare commonly used in drug and diagnostic development.All Azco products are supplied with comprehensive quality documentation. Our attention todetail assures your success.We are constantly adding to our product offering. If you do not see exactly what you arelooking for, contact your local representative or feel free to e-mail us atsales@azcobiotech.com. Where Are We? 3626 Ocean Ranch Blvd. Oceanside, CA 92056 Toll Free: (866) 706-6808 Page #: 33 Page #: Call us at +1-858-259-9528 or visit www.azcobiotech.com
  4. 4. XOMICS™ Xomics™ Integrated Bioinformatics Solution With the advent of 2nd generation sequencing a large amount of sequence data is now available for a large number of species. Although the cost for sequencing has come down dramatically, at a rate ex- ceeding Moore’s Law, the cost of data analysis has continued to rise, where today the cost of data analy- sis accounts for over 50% of the total sequencing cost: Source: Sboner et al., Genome Biology 2011 12:125 doi: 10.1186/gb-2011-12-8-125 It is has been estimated that by 2020, the cost to sequence a human genome will be less than $1000, but the cost for data analysis will be over $6500! For targeted sequencing, the sequencing cost is even less, but the analysis is 3X to 5X the cost of sequencing. Many commercial facilities offer an exome se- quence for ~$500. Still, the problem is data analysis with costs ranging up to $2500. That is, until now! Azco, in partnership with Theragen Bio, has launched Xomics™ a personal bioinformatics solution de- signed, and priced, to greatly bring down the cost of downstream sequence data analysis in a scalable, customizable, easy-to-use, integrated solution. Xomics™ is a system you control, it is not a “cloud-based” solution. Rather, Xomics™ is a hosted solu- tion where the server and integrated bioinformatics software is in your office. So, your data is com- pletely under your control! Page #: 4 Call us at +1-858-259-9528 or visit www.azcobiotech.com
  5. 5. XOMICS™Integrated SolutionXomics™ includes optimized hardware along with fully customizable bioinformatics software to form anintegrated solution for personal bioinformatics that is installed in your laboratory or office, not a solutionin the “cloud”.The hardware consists of a personal “server” offered in three standard configurations, each configuration sized to meet your current analysis re- quirements. Additionally, each con- figuration can be further customized to meet your exact needs. The software is a complete, turn-key, solution that performs sequence align- ment and mapping, quality statistics, SNP calling (i.e. Single Nucleotide Polymophisms, insertions, deletions, translocation, copy number variation, etc.), genotype/phenotype associations, reports the medical relevance of SNPcalls, pharmacogenetic information, even phylogeny information. Everything you need to transform yoursequence data into useful, reportable information for research, pharmacogenomic, or personal genomicapplications.Xomics™ HardwareXomics™ server hardware is offered in three standard configurations that can be further customized tomeet your individual requirements. Additionally, Azco offers on-site installation and integration serviceto network the Xomics™ server with your existing computers. The three standard configurations are: Light - Contains processing power designed for light to moderate sized applications including; exome sequence analysis, or other targeted sequencing applications. Standard - The Standard version contains the processing power required for most moderate to large scale sequence analysis applications by combining CPU with GPU processors. The applications in- clude; whole genome sequence analysis, exome sequence analysis, RNA-Seq plus others. Pro - The Pro version offers the same processing power as the standard, but includes additional stor- age to provide you the disk space required to store the data generated by large sequencing applications from hundreds of analyses.Each configuration can be further customized to meet your specific requirements. With Xomics ™, youcan start light and upgrade as your needs require. Page #: 55 Page #: Call us at +1-858-259-9528 or visit www.azcobiotech.com
  6. 6. XOMICS™ Below is a table that highlights the features of each of the standard configurations. Intel Xenon nVidia GPU Hard Disk Model RAM (GB) RAID (TB) CPUs (cores) (cores) (TB) Light 2 (8) ———— 48 6 ———— Standard 3 (12) 4(1792) 96 24 ———— Pro 3 (12) 4 (1792) 96 24 100 Why GPUs? CPUs (central processing units) consist of a few cores optimized for serial processing, while GPUs (graphical processing units) consist of thousands of smaller, more efficient cores designed for parallel processing. Serial portions of the application run on the CPU while parallel portions run on the GPUs. For processing the large amount of data generated from whole genome sequencing, using both CPUs and GPUs provides exceptionally fast, efficient processing. Below shows a graphic that compares CPU alone against using the combination: Sequence Alignment and Scoring CPU: 100 core cluster GPU: nVidia Tesla c2075X4 Raw Data: 100Gbase Human Exome (30X coverage) The use of both CPUs with GPUs allows the same data to be processed in one- tenth of the time, providing you the processing power of a supercomputer in a desk-side workstation at a very low cost! The exact configuration of your server can be optimized to meet your needs and networked to your existing se- quencers and bioinformatics systems. Additionally, with the use of “green” technology, these servers use very little electricity, making them very inexpensive to run, saving you money! Page #: 6 Call us at +1-858-259-9528 or visit www.azcobiotech.com
  7. 7. XOMICS™Xomics™ BioInformatics SoftwareThe real power of the Xomics™ solution is in the software. Xomics™ is a Microsoft Windows based applica-tion designed to allow you to easily process the data generated from all commercial 2nd and 3rd generationsequencers, using simple point-and-click commands. Your sequencer just needs to be able to output resultsin industry standard fastq format. Xomics™ reads in the fastq files generated by the sequencer and then...  Performs sequence alignment  Maps the sequences to a reference genome  Performs sequence quality metrics  Performs SNP calling -including SNPs, insertions, deletions, translocations  Determines Copy Number Variations  Performs and reports genotype to phenotype associations for human genome data  Determines the medical relevance of the SNPs called for human genome data  Determines pharmacogenomic characteristics based on the SNPs determined for human genomes  Determines the phylogeny of the human genome sequenced  Allows for comparison of one or more sample sets  Plus much more!So, out of the box, Xomics™ provides a complete set of features to meet most genome analysis needs, especiallyfor human genome sequence data.Xomics™ software can also be further customized to meet your specific needs. You can customize Xomics™ to: Directly interface with your sequencing platform, laboratory information system or other bioinformatics sys- tem. Produce reports that contain the information you and your clients require in the format you prefer. To perform the special data processing you require for your research on your specific genome whether it be plant or animal!Any need you have, Xomics™ is flexible enough to help. Page #: 77 Page #: Call us at +1-858-259-9528 or visit www.azcobiotech.com
  8. 8. XOMICS™ Easy and Intuitive User Interface Xomics™ is designed from the beginning to be intuitive and easy to use. From the main screen, simply drag your sequence files to the queue and your data is automatically processed. The time re- quired for the system to process your data depends on the hard- ware configuration selected. For a human exome, data process- ing can be finished in as fast as a few minutes! Once processing is complete, simply click on the “Analyzed Results and Comparison” tab to review your results! Sequence Alignment, Mapping and Quality Metrics After you’ve selected your file, Xomics™ maps the base calls from your sequencing run to the reference genome you’ve selected. It determines for you the quality of each read from the sequence you’ve provide and outputs the quality statistics for each read (i.e. Q score). It also provides you data to show the total reads, mappa- ble reads, depth of coverage used for each read, plus a lot of addi- tional quality information to assure you that the reports you gener- ate are valid and reliable! Sequence Alignment, Mapping and Quality Metrics Xomics™ provides you detailed information on all Genetic Variations found against the reference genome in your genome. Xomics™ provides complete reporting on the location and type of variation; SNP, insertion, deletion, translo- cation, transversion, insertion/deletion lengths, etc. It also provides quality information on the variations called. Additionally, you can not only compare your sample to a reference genome for variation calling, you can com- pare one sample to other samples, for example normal tissue to diseased tissue, or drought resistant grain to non-drought resistant, to determine somatic versus he- reditary mutations or quickly identify the genotype you are looking for. This feature will help you understand the variations that are relevant to the disease or phenotypes you are researching. Page #: 8 Call us at +1-858-259-9528 or visit www.azcobiotech.com
  9. 9. XOMICS™Genotype/Phenotype Association with Medical RelevanceXomics™ provides data evaluation tools that are color-coded to allow you to quickly pick out the datathat is relevant. Red indicates high risk, yellowinidicates caution and blue means low risk. When itis relevant, Xomics™ provides you extensive infor-mation on why the mutation is relevant includingdisease predisposition and probability. It even pro-vides you the PubMed link to reference so that youcan easily access additional details.With Xomics™ detailed annotation tools, you canquickly scan through an exome or a whole genometo get the information that’s important to you andyour client. Additionally, all of the annotations areprovided in the included reporting package. Or, wecan customize a report that meets your specific re-quirements.All the advanced information you need from your genome sequence, at your fingertips!Ancestry and Phylogeny InformationWith Xomics™ you can even trace the origin of your genome or exome. Xomics ™ provides you tools to see the racial admixture of your sample as well as follow the geographical origin of your genome from the beginning to pre- sent. This is not only a useful feature, but fun too! Xomics™ is designed to provide you with all of the information you or your custom- ers will ever need from the genome ana- lyzed and make the discovery easy. Page #: 99 Page #: Call us at +1-858-259-9528 or visit www.azcobiotech.com
  10. 10. XOMICS™ Summary Integrated Solution Xomics™ is the only integrated Next Generation Sequence analysis solution that provides you the power of a supercomputer through massively parallel processing in a desk-side workstation optimized with state-of-the-art BioInformatics software to provide complete analysis and annotation for your sequencing experiments in a cost effective package. To learn how Xomics™ can complete your sequence analysis workflow, contact your Azco Biotech sales representative or visit us on the web at www.azcobiotech.com. Page #: 10 Call us at +1-858-259-9528 or visit www.azcobiotech.com
  11. 11. XOMICS™ NOTES_______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ Page #: 11 Page #: 11 Call us at +1-858-259-9528 or visit www.azcobiotech.com
  12. 12. AZCO SERVICES Azco Service Azco backs up all of the instruments and bioinformatics systems we sell with “world-class” customer ser- vice. And after your warranty ends, Azco is still there to protect you. Azco offers a variety of service plans and options to meet your specific needs. Our most popular plans is the “Azco Premier Service Plan”. This is an “everything included plan” which begins with an annual pre- ventative maintenance visit, then should anything fail you are provided very rapid repair based on priority scheduling that includes all parts, travel, labor, everything, plus you receive unlimited telephone technical and applications support! Another very popular plan is Azco’s PM only plan. This plan is priced very reasonably and designed to get your instrument running in tip-top performance. Then, should anything fail, Azco will repair you system at a greatly reduced rate with priority scheduling, with this plan you also receive unlimited telephone and email technical support. Other popular services offered by Azco include paid day service, where we fix your instrument on- demand, laser change service, all parts, travel and labor in one reasonably priced package, on-site and mail in instrument refurbishing. Please call us for your specific needs. The instruments Azco services include:  Sequencers -ABI 377, 310, 3100A, 3100, 3130, and 3130xl  Synthesizers -Oligo-800, Oligo-96, Oligo-192, Dr.Oligo, OligoMaster, ABI 391/392/394, Expedite, ABI 3400, ABI 3900, most other brands.  Real-Time PCR -ABI 7000/7300/7500/7900, Agilent MX3000/3005, BioRad iCycler Plus others, please call. Genome Sequencing Have a genome you need sequenced, simply provide us the cell and we will do all of the work for you in- cluding library construction, amplification and sequencing followed by extensive data processing and an- notation using Xomics™ bioinformatics systems providing you complete reporting for your genome. Or, if you have a genome sequencer, we would be happy to perform the sequencer-ready library construction for you or downstream data processing. Please call for details. Azco Consulting Finally, Azco can help you with all of your application needs by providing consultants with years of ex- perience to help you optimize your bioinformatics integration, sequencing application, optimize synthesis, modification or purification. We can customize the solution to meet your needs. Please enquire to find out more! Page #: 12 Call us at +1-858-259-9528 or visit www.azcobiotech.com
  13. 13. AZCO SERVICES NOTES_________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ Page #: 13 Call us at +1-858-259-9528 or visit www.azcobiotech.com
  14. 14. LEGAL NOTICES Page #: 14 Legal Notices Azco Biotech, Inc. makes no warranties either expressed or implied as to the accuracy or appropriate- ness of this data and expressly excludes any liability upon Azco arising out of its use. We recommend that the prospective users determine for themselves the suitability of Azco materials and suggestions for any use prior to their adoption. Software screens and features will change from time to time; so, the actual product screens and features may be different than those represented herein. Azco makes no warranties as to the that all of the fea- tures described herein will be in the product ‘as sold’. Material Safety Data Sheets outlining hazards and handling methods are available upon request. They can downloaded at www.azcobiotech.com Amberchrom, Ambersynth and Amberlite are all trademarks of the Rohm and Haas Company, Philadel- phia PA., Texas Red is a registered Trademark of Invitrogen Inc., Carlsbad, CA., Hairpin-It is a trade- mark of GenePharma Co., Ltd, Shanghai, China, Dr. Oligo is a Trademark of Biolytic, Inc., Newark, CA, ABI, TaqMan, and all instrument models referenced are trademarks of AppliedBiosystems, Inc., Foster City, CA, NanoPOP is a trademarks of MC Labs, San Francisco, CA TQ, TF are trademarks of ABD Bioquest, Sunnyvale, CA, Xomics™ is a trademark of Theragen Bio, Seoul, Korea Call us at +1-858-259-9528 or visit www.azcobiotech.com
  15. 15. TERMS AND CONDITIONS Page #: 15 Azco Biotech, Inc General Terms of SaleParties: Azco Biotech, Inc. is hereinafter referred to as “Seller” and the customer is hereinafter referred to as “Buyer”, collec-tively Azco and customer are referred to as “Parties”.Agreement: A quotation is provided as an offer by Seller, issuance of a purchase order or payment by the Buyer is consideredacceptance of the offer and acceptance of the foregoing terms. The supply of products by Seller and payment by Buyer consti-tute mutual consideration to support the promises and creates a binding contract between the Parties.Price: The price agreed to between the Parties is provided to Buyer via Seller’s quotation, either formal or informal, the pricesupplied is in U.S. Dollars and unless otherwise agreed does NOT include shipping. When no price quotation is supplied, theprices on Seller’s web-site will be used.Payment: Seller’s standard payment terms for goods sold within the U.S. are net due 30 days after shipment of the order bySeller. Seller’s standard payment terms for goods shipped outside the U.S. are 100% prepayment prior to shipment. For Cus-tom Manufactured products, such as the Oligo 96/192, Xomics™ or OligoArray systems, Seller requires 50% with purchaseorder and net upon shipment by Seller to Buyer.Shipping: Seller provides all products E.X.W. origin. Risk of loss passes to Buyer upon transfer of goods to a common carrier.Seller’s standard shipping term is prepay and add costs to the final invoice. It is Buyers responsibility to specify insurance.Shipping charges include the cost of shipping along with any packaging or crating charges.Taxes and Duties: Sales taxes, duties and other Government imposed tariffs are the responsibility of the Buyer. Seller willcharge sales tax in the State of California and add this tax to the invoice.Irrevocable Agreement: Once Seller receives the down payment from Buyer towards the production of a Custom Manufacturedproduct, or the purchase order if no down payment is required, the agreement becomes irrevocable and is binding on the Partiesas well as their successors and assigns in interest. Custom Manufactured products are product that are not routinely stocked bySeller and made to requirements provided by Buyer, these products include, but are not limited to; Custom Xomics ™, Oligo 96,Oligo 192, OligoArray, custom dyes or phosphoramidites, and any other instrument or reagent made to the Buyer’s require-ments.Returns: Buyer may return products within 30 days after shipment by Seller for any reason subject to a 25% restocking fee.Custom Manufactured products, such as the Oligo 96/192 or OligoArray systems, are NOT returnable, once the down paymentis received by Seller, the order is irrevocable.Warranties: Seller expressly warrants that all goods supplied by Seller will conform strictly to the specifications, designs,drawings or samples provided by seller and are free from defects in material and workmanship, are merchantable and are fitONLY for their intended use. Most instruments provided by Seller include warranties, the length of the warranty will be speci-fied on the quotation and agreed to between the Parties. Should any part fail during the warranty period due to normal wear andtear, the part will be replaced by Seller free of charge. Inside the U.S. Seller will include labor and travel expenses with thewarranty. Outside the U.S. borders, unless otherwise agreed to, Seller’s warranty does NOT include travel and labor chargesand is PARTS ONLY. Sellers warranties exclude failures due to user negligence, or unforeseeable acts such as floods, fire,earthquake, acts of terrorism, etc. Sellers warranties also specifically exclude consumable parts. The list of consumables isunique to each instrument and will be provided to Buyer at time of sale. Other than the warranties discussed supra, Sellermakes no other warranties either express or implied including warranties of merchantability or fitness for intended use.Research Use Only: All reagents supplied by Seller are intended for Research Use Only. Use of products for diagnostic ortherapeutic use may be covered by proprietary rights not included by Seller to Buyer.Seller Liability Insurance: Seller represents that it maintains a valid Liability Insurance Policy with Scottsdale Insurance. Thelimits of liability are: $1,000,000 per incident and $2,000,000 aggregate. Buyer may be named as an insured, Seller will pro-vide a certificate representing Buyer as a named insured, the fee to be a named insured is $150.Subcontractors and Assignments: Seller retains the right to assign it’s duties under this and all agreements to subcontractors.All other rights and liabilities of the Parties remain in full force and effect with any assignment.Integration: This agreement between Buyer and Seller represents the entire agreement of the Parties and supersedes all otheroral or written agreements between the Parties.Disputes: Disputes between the Parties will first be negotiated between the Parties. Should good faith negotiations fail, eitherparty may file suit in a court of competent jurisdiction WITHIN THE STATE OF CALIFORNIA. All disputes shall be inter-preted and governed in all respects according to the laws of the state of California.Remedies: The Remedies between the parties is LIMITED to the value of the agreement. In no instance will Seller be liable toBuyer for Compensatory , Consequential or Punitive damages exceeding the value of the agreement between the parties. It isunderstood between the parties that Buyers loss of income or business opportunity due to delays or breach in performance bySeller are too speculative and are not compensable. If Buyer refuses to accept Sellers performance for any reason, after notifi-cation that Seller is ready to perform, Buyer agrees to pay Seller a either a 25% restocking fee or agrees to forfeiture of Buyersdeposit, whichever is greater. Call us at +1-858-259-9528 or visit www.azcobiotech.com
  16. 16. Azco Biotech, Inc.  Western Europe3626 Ocean Ranch Blvd. Azco Europe Ezequiel CoelhoOceanside, CA 92056 European Sales DirectorToll Free (866) 706-6808 Lisbon, PortugalTel (858) 259-9528 Mobile.+44 703 187 4691 Office. +44 870 490 3814Fax. (858)568-9078 Email: Ezequiel@azcobiotech.comEmail. sales@azcobiotech.comWeb. www.azcobiotech.com  Eastern Europe UAB Neokon BaltijaAzco International and Distributors Tomas Vaitkevicius Lithuania, Visaginas Taikos 10/12 LT-31107 China Mob.: (+370)685-58-796 Azco China Tel.: (+370)685-69-883 Bin “Frank” Zhang E-mail: neokonas@gmail.com & neokon@tts.lt General Manager 江苏省常州市常武中路801号常州科教城惠 研楼北楼5楼2520室  Turkey Mobile: 86-13881976869 Tel: 86-519-81001585 Tez Ileri Teknolojirler ve Savunma Sanayi Email: frank @azcobiotech.com Ticaret Ltd. Sti Pinar Demirtas South America Bilkent Plaza A3 Blok No: 32, Bilkent Ankara TURKEY Gentech Genetics & Technology Tel.: +90312 266 24 70 Jairo Alberto Colorado Castaño E-mail: info@tez.com.tr Carrera 46 No 48C Sur 40 Int.102 www.tez.com.tr segundo piso. Ciudadela Real Envigado - Antioquia - Colombia Tel: (57) (4) 2713885 - 2713768 - 2710206  Korea & Japan Email: gerencia@genetechcolombia.com Clinomics Byong Kim, PhD India B-601, Tweenpark officetel,1134-4, Inkye-dong Suwon, 442-835, Shrimpex Biotech Services Republic of Korea Thomas David Kumar Mobile: 010-8485-7697 76, East Coast Road, Sholinganallur Email: bckim00@gmail.com Chennai, TN, India, 600119 Tel: +91-44 2453 0845/46/47  Saudi Arabia Mobile: +91 98402 82825 www.shrimpex.in Constant Trading Activities E-mail: shrimpex@shrimpex.in Hasan Ibrahim P.O. Box 20451, Jeddah 21655 Saudi Arabia Tel : 698-7788 Fax : 682-3740 Mobile : 054338612 - 054338617