FAQ

Software

Search through our support documentation and FAQs for ArcherDX, now Invitae, products and services.

Archer® Analysis Unlimited (AAU) (Cloud-based)

Pros:
  • No need to purchase hardware
  • No need for server maintenance
  • No installation needed
  • Private cloud instance
  • Performs version updates upon request
  • Updates are in-line and preserve previous samples
  • Optimized computing performance
  • HIPAA and GDPR certified
  • Expandable computing resources, only pay for what you use
  • Run hundreds of samples concurrently
  • Automatic notifications when storage runs low
  • 1.5TB free space with option to purchase more
  • Automatic backups run every 3 days
Cons:
  • Nominal Instance setup fee
  • Nominal sample processing fee
Virtual Machine (VM)

Pro:
  • No per sample processing fee
Cons:
  • Expensive up-front cost for hardware
  • Less expensive servers have less throughput→ delays time to data
  • Service contracts for hardware
  • License to VMware hypervisor
  • Supports only VM installation, nothing else
  • Requires access to internal IT resources
  • Server Setup, VM installation required
  • Maintenance and administration required: storage, backups, security, networking, permissions
  • Version updates performed by customer
  • Previous data does not port over to new version
There are four ways you can access Archer® Analysis:
  1. You can use our live demo site at: analysis.archerdx.com. However, this is meant for training and demonstration, and is not for analysis of confidential samples. It is also used by other customers and staff and may become very backed up.
  2. The recommended method is to download the Archer® Analysis virtual machine. You will need to install virtualization software (VMware) and download our .ova file, which can be imported by the virtualization software.
  3. You can purchase Archer® Analysis Unlimited, which is a private cloud-based instance of Archer® Analysis where you pay only for the data you use. Contact technical support at [email protected] for more details.
  4. We have the Archer® Analysis Demo Site (https://demo.analysis.archerdx.com/), that is meant to be used as a pre-sales tool.
Contact Technical Support for further information and to request the user guide.
Yes, we do offer a standalone version of Archer® Analysis for purchase.

Analysis Unlimited is a highly scalable, private cloud-based instance of Archer® Analysis. With this solution, your fees are based on your use.

Contact your local business development manager or Technical Support.
Yes, this is one of the benefits of using virtual machine (VM). You can have a virtual machine with each version of the software enabling version lock-down and ease of validation.

However, there is no way to migrate data from one version to the other. So, if you are keeping older data after updating to a new version of the software you will need to keep the older version in order to access it, or you will need to re-process the FASTQ files with the new version of the software.

Assay Marketplace – A simple and intuitive tool that allows customers to browse, customize, and order from our vast catalog of predesigned panels and gene modules. All primer designs available on Assay Marketplace are generated using a purpose built algorithm to perform optimally in the context of AMP Chemistry and with the intended input material fragment length. Primers are wet-lab tested and balanced to achieve consistent performance across functionality, specificity and coverage metrics.

Assay Designer services – These panels are built from a combination of expertly reviewed de novo designs and predesigned primers. De novo primers are designed using a purpose built algorithm to perform optimally in the context of AMP Chemistry and with the intended input material fragment length and reviewed by an expert scientist.

Designer Pro services – For Designer Pro panels, the Assay Development team works closely with the customer through the entire course of development from target selection and curation through design optimization. Pro panels are iteratively tested in the lab. During the course of testing, primers are redesigned or rebalanced to meet panel performance given the customers needs. Input amounts, PCR cycling, and chemistry options are optimized. Due to the resources required for such development the expected turn around time from PO receipt to panel shipment is 8-12 weeks. The minimum first order size is 144 reactions. Designer Pro cost structure includes one time in silico design and functional testing fees, as well as per reaction assay purchased cost. The fees associated with in silico assay design and functional testing are project dependent and are invoiced at the completion of each development phase.
Custom panels do not require a change to the workflows’ protocols. The only variables are the reagent volumes, cycling conditions and recommended reads which are communicated in a custom Product Insert.
Custom panels do not require a change to standard Archer Analysis settings. A custom GTF will be provided and the appropriate analysis pipelines will be listed in the custom Product Insert.
We have yet to find a limit to the number of genes or primers that comprise a single panel. With the current analysis version (v6) users may experience long analysis times as panel size and read requirement increase.

We currently do not support panels larger than 7,000 primers for standard application of 5-3% VAF sensitivity, and larger than 2,000 primers for low allele frequency application.

We do not clinically validate RUO assays. Designer Pro and Catalog panels are functionally tested and primer performance is optimized iteratively. Assay Designer panels are not functionally tested in the lab prior to shipment, however we maximize the use of functionally tested designs where appropriate.
AMP panels are highly modular. Independent functionality of primers means that content can be added to or removed from existing panels without compromising assay performance.
A customer can add SNPID primer module to any VariantPlex®, FusionPlex® and LiquidPlex™ assay.

The the primers in the current SNPID module target intronic and intergenic high frequency population single nucleotide polymorphisms. For this reason, when used in the context of FusionPlex panels, low DNA content in TNA library input will impact SNPID analysis functionality.

The minimum number of reactions a customer must purchase on the first order for an Assay Designer custom panel is 24.
The most important components in a new server for Archer® Analysis are the CPU, memory allotment, and the ability to use VMware ESXi as the host. For processors, you must be able to allocate one core for each concurrent sample. Memory will need to be allocated at 12 GB per sample. The VM is thin provisioned to 1 TB.

For example, if you wanted to be able to process ten samples concurrently you would need 11 processors (one extra for the OS is recommended for best performance), and 120 GB of memory.

Software Requirements

You will need a platform to host the Analysis VM. We strongly recommend VMWare ESXi as it will allow the best use of available hardware. VMWare Workstation or Fusion can be used for evaluation purposes but are not recommended for production workloads as ESXi will better utilize the underlying hardware and offers more administrative capabilities.

Memory (RAM) and processor (CPU) requirements

On a per-sample basis, you need to dedicate 12 GB of RAM and 1 CPU core to the VM. One additional core is needed for the OS as well for optimum performance. Please refer to the installation guide for full details. If you want to run multiple concurrent samples, you’ll need to dedicate multiples of these requirements accordingly (e.g. 4 concurrent samples requires 48 GB RAM and 5 CPU cores).

Storage (hard disk) requirements

The disk storage needs per-sample are variable; panel and sample quality affect storage significantly. The best way to determine this is to run several of your own samples and determine the approximate resulting per-sample requirement. The VM itself comes with a data partition that is thin provisioned and 1 TB in size. If you end up needing more than 1 TB of space, then you could add more space to the VM using local storage or use a separate storage location, such as a NAS server or other file storage provided by your institution. Currently only NFSv3 without realm authentication is supported. If an external storage device is utilized for Archer® Analysis, the Analysis VM footprint will remain relatively small, less than 100 GB.

While you could create one login with one password, the better option is to create a group, then assign all the users to that group and give individual users the permissions that you would like to give them. This way you can still use the audit trail that is generated. This information is in the user manual and the admin for the VM would have to set this up.
VMware is required, ESXi is recommended.

For single workstation solutions VMware Workstation is recommended for Windows or Linux, and VMware Fusion is recommended for Mac.

VMware products can be purchased from vmware.com.
This functionality is enabled through a mechanism called “”Watched Folders””. A user with the appropriate permissions may configure a directory on the server for Archer® Analysis to monitor. When sample files or a folder of sample files appear in the watched directory, Analysis will automatically process these files according to the Watched Folder template.

Typically a demultiplexer would be responsible for performing read assignments and copying sample files to these watched folder locations. This is beyond the scope of Archer® Analysis itself but we can provide assistance in helping you configure this in some scenarios.

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