Products
Storage
Geneformics S
Compressed NFS filer
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Geneformics S is a server-software product that converts a configurable part of your NFS NAS capacity into an NGS-optimized file system, compressed by a factor of 10 and more for FASTQ files and 3 for BAM – with no loss of information. Geneformics S serves unmodified applications across the LAN with native-format NGS files through streamed, on-the-fly, high-throughput file compression and de-compression, while relying on your existing NFS server for raw capacity so you can make good use of past investment in storage and continue to buy from your favorite vendor. Geneformics S is delivered as a software package or an appliance in a range of configurations.
Geneformics H
Compressed HPC file system
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Geneformics H is a distributed, compressed-file system that leverages Geneformics’ advanced, NGS-tuned, lossless compression technology, coupled with NGS-optimized streamed file serving, to reduce by up to 90% the storage capacity taken up by NGS data, while providing seamless and high-throughput service to unmodified user applications running on your High Performance Computing (HPC) cluster. Installed on your HPC nodes, Geneformics H agents jointly use part of the capacity of your existing storage to implement an NGS-tuned compressed file system. Unmodified applications are served with native-format FASTQ and BAM files and remain completely unaware of compression. Background compression to cache and streamed, on-the-fly decompression ensure minimal performance impact on your pipeline.
Cloud
Compute and Transfer
Geneformics U
NGS-tuned, lossless compression toolkit
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Geneformics U is a flexible set of tools that adds the benefits of Geneformics’ NGS-tuned, lossless compression technology to any of your transfer or other processing tasks.
Geneformics U leverages Geneformics’ advanced, NGS-tuned, lossless compression technology, coupled with NGS-optimized streaming capability to reduce the size of FASTQ files by 10X and more (3X and more beyond ZIP) and BAM files by 3X.
Geneformics U relies on off-the-shelf hardware and standard, flexible Unix interfaces. It can therefore be easily integrated into any existing transfer workflow, bioinformatics pipeline or other data processing and management task.
Contact us to see how Geneformics U can easily fit into your workflow.
Technology
The science of Information Theory has proven that compression cannot be universal and highly-efficient at the same time. The ZIP family of algorithms, for example, is useful across a wide range of data formats but does not excel in any, NGS data included: ZIP will typically compress FASTQ files by 3X (size reduction by a factor of 3), while the BAM format uses blocked-ZIP to reduce the size of SAM files by 2.5X.
Leveraging deep understanding of the underlying bioinformatics as well as the sample preparation and sequencing operations that create FASTQ and subsequently BAM files, Geneformics was able to greatly improve on the performance of ZIP when it comes to the lossless compression of FASTQ and BAM data. Thus, our compression algorithm will compress FASTQ files by a factor of 10 and more (3 times and more beyond ZIP), and BAM files (which are already ZIP-compressed) by 2.5-3X.
When it comes to large scale, industrial-grade deployment, compression and decompression throughput is just as important as compression ratio. Geneformics’ compression technology provides that through a highly-optimized architecture, with efficient multi-threading allowing flexible scale-out of compression and decompression operations.
Geneformics’ compression technology supports random reading from compressed files: when an application needs to access a file segment at a random offset into a BAM file, the software will directly decompress the relevant part – without having to go back and start at the beginning of the file.
For maximum compatibility with de-facto standards, our compressed BAM files are CRAM compatible: they can be directly read as CRAM files, while still supporting 100% lossless decompression back to the bit-for-bit identical BAM version (which is not possible with standard CRAM).
Compressed, Streamlined Genomics Data
Geneformics C
Compressed, object-based NFS server
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Based on Geneformics’ NGS-tuned, streamed file compression and proprietary object-to-file technology, Geneformics C is a transparently compressed, NFS server for the cloud. Geneformics C is placed between your LAN-in-the-cloud (or Virtual Private Cloud - VPC) and the cloud infrastructure provider's object store (such as Amazon's S3). Compute instances are presented with an NFS server interface that allows unmodified POSIX-compliant applications to read and write native-format files, remaining completely unaware of compression. The Cloud Server, in turn, stores compressed data in object store, reducing by up to 90% the cost of cloud storage – with no sacrifice of reliability or durability.
Geneformics D
Distributed file system for the cloud
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Geneformics D is a compressed-file system for the cloud that leverages Geneformics’ advanced, NGS-tuned, lossless compression technology, coupled with NGS-optimized streamed file serving, to reduce by up to 90% the storage capacity taken up by NGS data, while providing seamless and high-throughput service to unmodified user applications.
Geneformics D nodes, installed on client compute instances, jointly implement a distributed, transparently compressed file system that scales out seamlessly with your compute infrastructure. Unmodified applications are served with native-format files, while background compression to cache and streamed, on-the-fly decompression ensure minimal performance impact on your pipeline. All file system data are kept in cloud object storage for maximum availability and reliability and optimal cost.
