Data storage and machine learning in the genomics era
Data storage and machine learning in the genomics era
Human whole genome sequencing is a cornerstone in the national precision medicine projects emerging in recent years. The sequencing of short reads of DNA has mainly been solved, so in the next decades three crucial questions must be answered: (1) How to store these massive amounts of data being generated every day from national and regional genomics lab, (2) What are the requirements to doing so, and (3) How do we analyse petabytes of genomic data?
Topics:
- Data storage considerations for the pharmaceutical industry, clinical genomics labs, and national genome programs
- Amount of data generated and stored
- Data safety and storage performance
- Combinations of Cloud and on-site storage
- Meeting the needs for a very fast and secure 1.1 PB data storage solution at SciLife Clinical Genomics in Stockholm; the data requirements for a population-scale genomic project in Scotland
- Machine learning on petabytes of genomic data
Details are as follows:
Date: November 19
Time: Whole day event; Rasmus will be presenting at 10:40–11:15.
Location: Charlottehaven, Hjørringgade 12C, 2100, København Ø
SciLife Clinical Genomics Stockholm lab acquires 1.1 Petabyte data storage from Leymus Genomics & DDN
SciLife Clinical Genomics Stockholm lab acquires 1.1 Petabyte data storage from Leymus Genomics & DDN
Leymus Genomics, in partnership with DDN, are now installing the DDN GS7K Data storage platform with 1 petabyte data storage for the SciLifeLab Clinical Genomics Stockholm lab.
As the NovaSeq and HiSeq X systems are becoming the new standard in leading genomics centers in the Nordic, so is the data output. An Illumina NovaSeq 6000 generates approximately 6 terabases in a full S4 two flowcell run over two days. This equates to very roughly 3 terabytes of data per day, or 1.1 petabyte per year. For the Nordic clinical lab, local storage sites for their NGS output is mostly the preferred option to ensure compliance and faster I/O i.e. access to and generation of data.
Bioscience 2019: Rasmus Brøndum is an invited speaker on big data storage in genomics at Aula Medica, Karolinska Institutet
Bioscience 2019: Rasmus Brøndum is an invited speaker on big data storage in genomics at Aula Medica, Karolinska Institutet
Human whole genome sequencing is a cornerstone in the new national precision medicine projects emerging these years and human whole genome sequencing in a clinical setting will be a valuable genomic application potentially replacing todays targeted genomic applications . The sequencing of short-reads of DNA has mainly been solved, and now in the next years two very crucial questions must be answered:
1. How to store these massive amount of data being generated every day from national and regional genomics labs?
2. What are the requirements?
Come join us in Sweden at Karolinska Institutet. The event is an excellent opportunity to meet and exchange ideas with fellow researchers and companies.
Details are as follows:
Date: November 7
Time: Whole day event; Rasmus will be presenting at 15:25–15:45.
Location: Aula Medica, Karolinska Institutet, Nobels väg 6, 171 65 Solna
Leymus Genomics to present at DMS2019 in Copenhagen
Leymus Genomics to present at DMS2019 in Copenhagen
Some of the benefits of LoopSeq® include:
- Uses your existing Illumina sequencer – no extra instruments
- Single-molecule sequencing
- Multiplex single-tube workflow
- Consensus error correction - error rates reduced 40x vs. standard short reads
- Full isoform mapping for transcriptome research
- True quantitative results due to transcript counting using UMIs and full-length reads
- Better resolution on species and strain level for microbiome research
Come join us in Copenhagen in Eigtveds Pakhus for Rasmus’s presentation. The congress is an excellent opportunity to meet and exchange ideas with fellow researchers and companies.
Details are as follows:
Date: November 11
Time: Whole day event; Leymus will be presenting at 15:15–15:40 in Room 2 on the 2nd floor.
Location: Eigtveds Pakhus, Strandgade 25G, 1401 Copenhagen
LoopSeq seminar in Oslo October 10th by Leymus Genomics
LoopSeq seminar in Oslo October 10th by Leymus Genomics
On the 10th of October, Rasmus Brøndum from Leymus Genomics will be presenting an exciting new synthetic long-read sequencing technology that functions on existing short-read Illumina® sequencers. LoopSeq®, developed by Loop Genomics, is an innovative sequencing technology that provides previously inaccessible layers of information from Illumina®-generated sequences. This enables a wide variety of diverse sequencing applications, including sequencing of microbiomes, transcriptomes, targeted amplicons, and more.
Some of the benefits of LoopSeq® include:
- Uses your existing Illumina sequencer – no extra instruments
- Single-molecule sequencing
- Multiplex single-tube workflow
- Consensus error correction – error rates reduced 40x vs. standard short reads
- Full isoform mapping for transcriptome research
- True quantitative results due to transcript counting using UMIs and full-length reads
- Better resolution on species and strain level for microbiome research
Come join us in Oslo at the Ullevål University Hospital for Rasmus’ talk. Number of attendees will be limited so be sure to email us (kristine@leymusgenomics.com) if you’re interested. Details are as follows:
Date: October 10
Time: 13:00 – 14:30
Location: Ullevål University Hospital, Labbygget, Building 25, 1st floor, Green Auditorium. Kirkevejen 166, 0450 Oslo.
Leymus Genomics and Loop Genomics at ESHG 2019 in Gothenburg
Leymus Genomics and Loop Genomics were at ESHG 2019
Thanks again to all the wonderful people who visited us at this year’s European Society of Human Genetics (ESHG) conference in Gothenburg. We were overwhelmed by all the positive feedback Leymus Genomics had with Loop Genomics’ stand, and we enjoyed talking to all of you. Indira Wu, Loop’s Director of Molecular Biology, had a sold-out presentation at ESHG on the principles and applications of the LoopSeq kits. If you missed it, or would like to hear it again, please see the video below or you can download the slide deck. The last 10 minutes is a very exciting Q&A – we know it’s mind-blowing (!) that you can actually do long-read sequencing on an Illumina sequencer. ESHG said they’d never seen such a turnout for a first-time presenter at a satellite meeting!
Slide deck: Loop Genomics ESHG slide deck
Loop Genomics has developed a synthetic long-read sequencing technology that leverages existing Illumina® short read sequencers coupled with LoopSeq® barcoding technology to enable single-molecule, long-read sequencing on any Illumina® infrastructure. The benefits include:
- Synthetic long-read NGS kit
- Uses your existing Illumina sequencer – no extra instruments
- Multiplex single-tube workflow
- Consensus error correction – error rates reduced 40x vs short reads
- Full isoform mapping for transcriptome research
- True quantitative results due to transcript counting using UMIs and full-length reads
- Better resolution on species and strain level for microbiome research
You can learn more here: https://www.loopgenomics.com/learn
Leymus Genomics is the distributor of the LoopSeq kits in northern Europe, so please get in contact with us if you feel you or your company could benefit from getting long-read data from your Illumina short-read sequencers with just a kit including free and intuitive software – no additional hardware.
New hire at Leymus Genomics! Please welcome Kristine Kjær, who will be joining the team as the scientific sales and training contact responsible for Loop Genomics. Kristine has a MSc in Molecular Biology and will be supporting our customers in how to get the best possible data from the LoopSeq kits. With the right support our customers can get the full benefits of producing high quality long-read data on your existing Illumina short-read sequencers. LoopSeq allows you to:
- do single-molecule counting
- multiplex your workflow
- the kits include a full report + long-read FASTQ file
If you need more information about how Loop can help your research, need training in how to use the kits, or want to chat about how the technology works, just contact us.
We invite you to hear the talk by Loop Genomic's Indira Wu at ESHG 2019
Hear the talk by Loop Genomic's Indira Wu at ESHG on Monday, June 17, 15:00 - 16:30 in Room A-4.
- Synthetic long-read NGS kit
- Uses your existing Illumina sequencer – no extra instruments
- Multiplex single-tube workflow
- Consensus error correction - error rates reduced 40x vs short reads
- Full isoform mapping for transcriptome research
- True quantitative results due to transcript counting using UMIs and full-
length reads - Better resolution on species and strain level for microbiome research
Loop Genomics has developed a synthetic long-read sequencing technology
that leverages existing Illumina® short read sequencers coupled with LoopSeq®
barcoding technology to enable single-molecule, long-read sequencing on any
Illumina® infrastructure.
Indira Wu, the Director of Molecular Biology at Loop Genomics, will in her talk
explore LoopSeq® sequencing technology and how it provides previously
inaccessible layers of information from Illumina®-generates sequences,
enabling a wide variety of diverse sequencing application, including sequencing
of microbiomes, transcriptomes, targeted amplicons, and more.
DDN awards Leymus Genomics the prestigious partnership prize
DDN awards Leymus Genomics the prestigious partnership prize
Berlin, 11th of April 2019
We are looking forward to continuing the collaboration on installing the best data storage at scale for genomics, life sciences, and AI.
Leymus Genomics works to create value for genomic sites that need data storage with highly reliable performance and also the best priced data storage as demonstrated recently at the data storage project at SciLifeLab Clinical Genomics Stockholm.
Full length 16S Sequencing with short reads: Simpler, better & cost-effective
Full-length 16S Sequencing with short reads: Simpler, better & cost-effective
Leveraging your existing sequencing infrastructure, Loop Genomics improves the accuracy of 16S sequencing with our LoopSeqTM Complete and LoopSeqTM Select products.
With LoopSeq Complete and LoopSeq Select you get:
Enhanced performance
- More comprehensive species identification
- More accurate species classification
- More accurate relative species abundance
A cost-effective solution
- Uses your existing short-read sequencing infrastructure
- Requires no additional hardware
- Saves time and labor with a simple, streamlined workflow
Powerful technology
- Converts your existing short-read sequencer into a long-read, single-molecule counting instrument
- Smartly implements a synthetic long-read approach
- Increases sequencing accuracy (error rate <0.005%)
Discounted test kit
Available on request, or alternatively test as a send out of your samples.
Learn more
