Illumina reads. Medical search. Frequent questions

When I say rna-seq, i am talking about illumina, oxford nanopore, and pacBio. (biostars.org)
Oxford Nanopore long reads were combined with Illumina short reads to generate a high-quality ~ 858 Mbp genome assembly within 850 contigs with 46× long read coverage. (nature.com)

The researchers used a whole-genome shotgun sequencing strategy and constructed 37 paired-end libraries with an average read length of 52 base pairs. (genomeweb.com)
The panda project "shows the power of high-throughput sequencing and the use of shotgun combined with long paired-end reads," said Kjetill Jakobsen, leader of the consortium that recently sequenced the cod genome with 454 technology and a professor of biology at the Centre for Ecological and Evolutionary Synthesis at the University of Oslo. (genomeweb.com)
As I know, illumina begins sequencing from both 5 prime and 3 prime but why are there 3 prime bias? (biostars.org)
We also report SNV numbers for three additional O. australiensis genotypes based on Illumina re-sequencing. (nature.com)
8 provided an update to the OryzaGenome database which includes short-read sequencing data for several non-AA genome Oryza species. (nature.com)
This instance of BWA works with single-end sequencing reads. (atlassian.net)
San Diego-based Illumina is the world's leading maker of DNA sequencing equipment. (sandiegouniontribune.com)
San Diego gene sequencing giant Illumina announced an $8 billion deal Monday to acquire Grail Therapeutics, a Bay Area biotech once part of Illumina that is developing a blood test to catch cancer sooner. (sandiegouniontribune.com)
This deal is quite transformative for Illumina," said Dr. Phil Febbo, chief medical officer, as it shows that the gene sequencing giant is "a company that also cares about testing for providers and patients. (sandiegouniontribune.com)
Illumina estimates all forms of sequencing-based cancer testing, from screening the healthy to monitoring those who've been diagnosed, could be worth $75 billion by 2035. (sandiegouniontribune.com)
Illumina launched its accelerator program in 2014 to assist startups and early-stage companies working on next-generation sequencing applications. (genomeweb.com)
Each of the following platforms utilizes a different type of technology to sequence millions of short reads: 454 Sequencing, Illumina, and SOLiD. (wikipedia.org)
San Diego-based Illumina is a major supplier of next-generation sequencing systems for genetic and genomic analysis, while Grail is a health company developing blood tests to try to catch cancer early. (kron4.com)
Illumina, a leader in next-generation genomic sequencing technologies, and Invitae, a leading medical genetics company, have joined as founding partners. (bio-itworld.com)
Illumina is one of the few companies licensed by the FDA to perform whole genome sequencing (WGS) for medical diagnosis-other consumer products such as Ancestry.com , National Geographic's Geno 2.0 , and 23andMe , provide only a limited analysis. (3quarksdaily.com)
Illumina has launched software that facilitates whole genome sequencing for rapid identification of rare genetic diseases. (scienceboard.net)
June 18, 2020 -- Illumina has acquired BlueBee, a Dutch genomics analysis software firm that originated as a spinoff from Delft University of Technology, in an effort to boost its next-generation sequencing (NGS) capability. (scienceboard.net)
The purchase will also help Illumina lower the cost of storing, sharing, and managing genomic data from the company's installed base of more than 15,000 sequencing systems. (scienceboard.net)
Merck Serono and Illumina , Inc., announced a collaboration to expand the development of a universal next-generation sequencing-based oncology diagnostic for clinical trials of targeted cancer therapies. (analytica-world.com)
Our collaboration with Illumina around next-generation sequencing will enable us to perform genome studies at a pace unheard of a few years ago, and could lead to the development of several diagnostics," said Susan Herbert, Head of Global Business Development at Merck Serono. (analytica-world.com)
An average of 7 million reads were generated with approximately 21,526 genes mapped in each sample post-inoculation at 6 h (6 HPI) and 6 days (6 DPI) using RNA-sequencing technology. (frontiersin.org)
Our Lab has developed a pipeline to collapse near-duplicate reads resulting from Ultra Hight Throughput Sequencing (UHTS), specifically Illumina and 454. (stanford.edu)
As we are using Illumina sequencing platforms, we provide some general information below. (lu.se)
In addition, long-read sequencing of one representative XDR ST235 isolate identified an integron carrying multiple resistance genes (including bla VIM-2), with differences in gene composition and synteny from the P. aeruginosa class 1 integrons described previously. (who.int)
Due to the SARS-CoV-2 pandemic, recent work has focused on establishing qPCR assays, targeted Spike mutation analysis and whole genome Illumina sequencing of SARS-CoV-2. (lu.se)
Target sequence enrichment (48.48 Fluidigm Access Arrays) and sequencing were performed (Illumina Hi-Seq 2,500 instrument, v4 chemistry). (lu.se)
Our unit has instruments and resources for traditional Sanger Sequencing (ABI 3500) but also for the so-called Next-Generation Sequencing (NGS) based on the Illumina MiSeq platform. (lu.se)

What do Illumina HiSeq/MiSeq paired end reads look like? (stackexchange.com)
If it helps I have a read pair from one of my MiSeq runs below. (stackexchange.com)
v1.0.0 : 2021-02-16 (many thanks for suggestions and feedback to T. Stark, K. Lacek, B. Rambo-Martin, C. Paden, and J. Tognarelli) - Added SARS-CoV-2 to the experimental CoV module and performed optimization for MiSeq 2x150 PE reads. (cdc.gov)

Last week, the BGI team published results from de novo assemblies of two human genomes using the Illumina technology ( see In Sequence 12/8/2009 ). (genomeweb.com)
FLASH does) is not the same as 'sequence assembly from PE reads' (what MetaSPAdes does). (stackexchange.com)
If you want to learn more about sequence assembly, I suggest you read the sequence assembly wikipedia page. (stackexchange.com)
The cDNA sequence reads are assembled into transcripts via a short read transcript assembly program. (wikipedia.org)
Is there a reason that you are spending the time and money to do the second read when the first read gives you almost the exact same sequence information? (stackexchange.com)
Illumina can sequence a Gbp of data for \$7 - \$93. (stackexchange.com)
Nashville Biosciences LLC and Illumina Inc. today announced an agreement with Amgen to whole-genome sequence approximately 35,000 DNA samples. (vanderbilt.edu)
With revenue of just over $1 billion last year, Illumina sells machines that sequence the human genome. (sandiegofreepress.org)

Scientists at the Beijing Genomics Institute in Shenzhen reported this week in Nature that they sequenced and assembled a draft genome of the giant panda using only the Illumina Genome Analyzer platform and the SOAPdenovo algorithm for assembly. (genomeweb.com)
Eureka Genomics is launching its first Eureka Genomics Center in North America and will use the Illumina Genome Analyzer. (genengnews.com)
Through our collaboration with Illumina Accelerator, we hope to provide breakthrough startups with the resources, infrastructure, and support to transform their ideas into compelling consumer applications and services that make genomics relevant and accessible to every person based on their unique interests," Helix CEO Robin Thurston added in the statement. (genomeweb.com)
Illumina is like the Apple of the genomics business. (sandiegofreepress.org)

Illumina is the biggest biotech in town, and the acquisition, slated to go through by the second half of 2021, is one of the largest deals in San Diego biotech history. (sandiegouniontribune.com)
Illumina expects to debut Galleri in the second half of 2021, and it believes there is a huge and growing market for such tests. (sandiegouniontribune.com)
Grail, which was acquired by Illumina in 2021, developed a blood test that is intended to screen for multiple cancers. (medtechdive.com)
If Illumina had failed to close the takeover by Dec. 20, 2021, it would have needed to pay a $300 million termination fee and make a $300 million investment in Grail, on top of the $35 million a month it has been handing over this year. (medtechdive.com)
September 20, 2021 -- Illumina Ventures has raised $325 million for its second investment fund, which will support healthcare startups. (scienceboard.net)

The Galleri test uses Illumina sequencers to detect tumor-associated DNA modifications. (sandiegouniontribune.com)
Illumina CEO Francis deSouza said in January that its installed base was more than 22,000 sequencers. (yahoo.com)

The European Union on Thursday, Oct. 12, 2023 ordered U.S. biotech giant Illumina to undo its $7.1 billion purchase of cancer-screening company Grail because it closed the deal without approval of regulators in the 27-nation bloc. (kron4.com)
Illumina said it expects decisions on its appeals from the U.S. Court of Appeals for the Fifth Circuit by the end of 2023 and from the European Court of Justice in mid-2024. (medtechdive.com)
Thaysen, on the call, said Illumina expects "2024 results will look very similar to 2023. (medtechdive.com)

Wang said that the recent improvements to Illumina's platform would allow for increased read lengths that would have improved the assembly accuracy even more. (genomeweb.com)
Market analysts with investment bank Robert W. Baird & Co. expressed cautious optimism around Illumina's announcement, noting that, while it's a plus that Illumina already owns about 14 percent of Grail, it will take a while to see the deal pay off. (sandiegouniontribune.com)
Paired-end reads comes from opposite ends of a fragment (you could learn the reason it happens from Illumina's video ). (stackexchange.com)
PacBio provides longer read length than Illumina's short-length reads. (stackexchange.com)

We have updated fulcrum to be compatible with the new Illumina fastq output. (stanford.edu)
For demultiplexing ( FASTQ files ), you must supply Illumina compatible SampleSheet. (lu.se)

Yourgene (AIM: YGEN), a leading international molecular diagnostics group, announces that it has received CE-IVD marking for its Illumina-based IONA® test, the Company's flagship non-inva. (bionow.co.uk)

Grail spun out of Illumina in 2016 after researchers stumbled on an odd finding. (sandiegouniontribune.com)
Grail stockholders will get $3.5 billion in cash and $4.5 billion in shares in Illumina stock. (sandiegouniontribune.com)
Illumina said it is reviewing the order to sell Grail. (kron4.com)
Illumina announced the acquisition of Grail in 2020, but the commission said the company broke EU merger rules by completing the deal without its consent. (kron4.com)
The EU accused Illumina and Grail of knowingly and deliberately merging before getting clearance in what amounted to a vital infringement of the rules. (kron4.com)
Illumina must "restore the situation prevailing before" the acquisition, regulators said, and how Illumina divests itself of Grail also needs EU approval. (kron4.com)
The Federal Trade Commission ordered Illumina to sell Grail earlier this year after finding the merger would "stifle competition and innovation in the U.S. market for life-saving cancer tests. (kron4.com)
Illumina said Thursday it has retained advisers to prepare for a sale or capital markets transaction of its Grail cancer test unit. (medtechdive.com)
Illumina will be in contact with investment capital sources or potential purchasers even as it continues to appeal orders from regulators in the U.S. and Europe to divest Grail , CEO Jacob Thaysen said in his first earnings call as head of the company. (medtechdive.com)
Illumina is appealing a record fine imposed by the European Commission for closing the Grail transaction prematurely. (medtechdive.com)
The Federal Trade Commission has also ordered Illumina to divest Grail , after determining that its ownership would stifle competition and innovation in the U.S. market for life-saving cancer tests. (medtechdive.com)
Illumina reported a third-quarter net loss of $4.77 per share, which included goodwill and intangible impairments of $821 million related to Grail. (medtechdive.com)
In the year-ago period, Illumina lost $24.26 per share, including goodwill impairment of $3.91 billion for Grail. (medtechdive.com)
Illumina has closed its $8 billion takeover of liquid biopsy player Grail despite an ongoing regulatory review by the European Union and a pending U.S. Federal Trade Commission administrative trial. (medtechdive.com)
For now, Illumina is holding off on integrating Grail pending the regulatory and legal reviews. (medtechdive.com)
The question of whether Illumina has time to get regulatory and legal clearances before closing the Grail deal has hung over the company since the Commission opened its in-depth investigation into the takeover last month. (medtechdive.com)

While the Commission's 90-day investigation pointed to a late November conclusion, Illumina now expects the process to be completed early next year. (medtechdive.com)

On Feb. 8, it was recommended by Illumina to its shareholders to reject the initial offer. (ibtimes.com)
On the call, Cowen's Doug Schenkel pushed deSouza to discuss the risk that Illumina is "further damaging" its relationship with the U.S. government, leading to negative effects on future strategic endeavors, and "causing distraction and wasted efforts that are ultimately not in the best interest of Illumina shareholders. (medtechdive.com)

And Illumina holds its dominant position at an enviable moment in history, as we're heading into a scientific golden age when human genomes will be sequenced for $1,000 or less. (sandiegofreepress.org)
Helpful for long genomes + reads that Smith-Waterman can't handle so well. (cdc.gov)

Meanwhile, the Mayor signs a ten year deal that would keep Illumina here till 2024. (sandiegofreepress.org)

We estimate that, with Illumina acceleration, the Galleri test can conservatively save 10,000 additional lives in the U.S., and additional lives in the EU over the next 9 years. (medtechdive.com)

NEW YORK (GenomeWeb) - Helix announced today that it has partnered with Illumina Accelerator to provide support to new companies developing DNA-based products for the consumer market. (genomeweb.com)
Through the partnership, Helix will now offer resources to certain Illumina Accelerator startups that are working on consumer-focused DNA products. (genomeweb.com)
Illumina has chosen seven companies to join the first global cohort of Illumina Accelerator, its startup incubator that partners with entrepreneurs to. (scienceboard.net)

Emedgene and Illumina have partnered to interpret genomic data for rare diseases. (scienceboard.net)

I heard ONT has 3 prime bias the most, then illumina, and then pacbio. (biostars.org)
What reasons are there to choose Illumina if PacBio provides longer and better reads? (stackexchange.com)
Sounds like PacBio can do whatever Illumina platform can offer. (stackexchange.com)
Edit, I just found a google sheat with prices that seems to be frequently updated, seems that the ratio still holds Illumina short reads ~10x cheaper than PacBio. (stackexchange.com)

Roche, the Swiss drugmaker, has announced that it has extended its tender offer to acquire all outstanding shares of Illumina, Inc., for $44.50 in cash per common share until March 23. (ibtimes.com)
The offer for Illumina was due to expire Feb. 24 and the other terms for the extended offer will be remaining the same, according to Roche. (ibtimes.com)
Roche announced the proposed $5.7 billion takeover January 25 and since then Illumina shares have traded above the offer price. (ibtimes.com)
Meanwhile, Illumina has instated a strategy termed as poison-pill with the intention of diluting the stake of Roche in the company. (ibtimes.com)
Roche, which is the world's biggest maker of cancer drugs, is targeting to expand the market share of its diagnostic products by taking over Illumina. (ibtimes.com)

In 2007 GenomeWeb News reported that Illumina signed a fifteen year lease for a new 84,000-square-foot facility currently under construction in San Diego that will enable it to expand its laboratory and office workforce. (sandiegofreepress.org)

illumina-plugins-1.0.tar.gz ( 80.4 KB ) - added by Nicklas Nordborg 16 years ago . (lu.se)

While Illumina said the European Commission will likely respond by trying to impose a fine of 10% of its consolidated annual turnover, CEO Francis deSouza told investors the deal will save lives. (medtechdive.com)

Added ENFORCE_CLIPPED_LENGTH to enforce minimum read length during QC post IRMA adapter trimmed Illumina PE reads. (cdc.gov)

You are probably looking for methods that talk about complicated, computationally complex assembly algorithms and graphical methods for summarizing lots of short reads. (stackexchange.com)
Short read assemblers generally use one of two basic algorithms: overlap graphs and de Bruijn graphs. (wikipedia.org)

In return Illumina promised to keep a number of jobs in San Diego for the term of the agreement. (sandiegofreepress.org)
It doesn't sound like Illumina has plans to abandon San Diego any time soon. (sandiegofreepress.org)
Mark Cafferty, president and CEO of the San Diego Regional Economic Development Corp .- a key organizational player in reaching the Illumina agreement - suggested that Memphis was the big player here in luring Illumina away. (sandiegofreepress.org)
Local news NBC 7 San Diego reported that "the deal" was announced on July 15, 2014: "Under the 10-year agreement, Illumina will keep 300 middle-class manufacturing jobs in San Diego and receive a tax break up to $1.5 million. (sandiegofreepress.org)

I have some shotgun Illumina paired-end data from a gut microbiome project I'm working on. (stackexchange.com)

Illumina has partnered with investment firm Sequoia Capital China to launch a new collaboration designed to create an incubator for startup companies. (scienceboard.net)

Your libraries need to be compatible with requested Illumina platform. (lu.se)

This is the accepted method by this point for Illumina metagenomic data, because it is the method that is capable of handling the amount of small pieces of data in a tractable fashion. (stackexchange.com)
Illumina is making its SARS-CoV-2 data toolkit, a suite of data analysis tools and workflow functionality, free for researchers researching the virus. (scienceboard.net)
updated the Ebola and CoV modules to use MERGE_SECONDARY=1 v0.6.6 : 2017-04-13 - added "MERGE_SECONDARY" option, puts secondary data into the unmatched read pool for round 2. (cdc.gov)
For SNP experiments: Illumina SNP manifest files in CSV format, Illumina SNP raw data files from BeadStudio. (lu.se)

The study is one of the first in which researchers sequenced and de novo assembled a large mammalian genome using only short-read technology. (genomeweb.com)

The EU said the acquisition would squeeze out competitors and give Illumina too dominant of a position in the market. (kron4.com)

With the deal set to expire before regulators reached their decisions, Illumina has taken the potential risk that it will need to unwind the takeover down the line in response to regulatory opposition. (medtechdive.com)

begingroup$ What was the size of the library and what is the read length? (stackexchange.com)

I'm considering how to go about generating contigs from reads. (stackexchange.com)
But generally speaking, both programs are building different flavors of de Bruijn Graphs from metagenomic reads to generate contigs/scaffolds. (stackexchange.com)
To reiterate, simple read merging tools will not give you assembled contigs. (stackexchange.com)
We assembled the transcriptome of a clonal population of adult, aposymbiotic (dinoflagellate-free) Aiptasia pallida from ~208 million reads, yielding 58,018 contigs. (stanford.edu)

This package contains plug-ins for the Illumina platform. (lu.se)

The outcome of this research is a desk lamp inspired by nature, offering adjustable brightness, light color, and the capability for self-illumina- tion. (lu.se)

Longer reads offer better opportunity for genome assembly, structural variant calling. (stackexchange.com)

Illumina estimates that widespread adoption of the test could avoid 100,000 cancer-related deaths a year, and that 52 million U.S. adults could benefit from routine blood tests that detect a wide swath of cancers. (sandiegouniontribune.com)

NEBNext ® Multiplex Oligos for Illumina® are an essential piece of the NEBNext suite of library preparation products, available in several different configurations for use with NEBNext products or other standard Illumina-compatible library preparation protocols. (neb.com)

Illumina posted third-quarter revenue of $1.12 billion, flat with the year-ago period and down 5% from the second quarter, citing customer capital budget constraints and reduced demand from Russia and China. (medtechdive.com)

It is not worse than short reads for calling SNP/indels, quantifying transcripts. (stackexchange.com)

Would that be any reason for going with Illumina if PacBio's long reads can do everything and more? (stackexchange.com)

By ordering Illumina to restore Grail's independence, we ensure a level playing field in this crucial market to the ultimate benefit of European consumers," he said. (kron4.com)

The EU already slapped a $475 million fine on Illumina over the summer for jumping the gun on the acquisition without its consent. (kron4.com)
With the latest round of investments, Illumina Ventures has built up a genomic-focused fund of $560 million. (scienceboard.net)

Wang said the study showed that short-read technology such as the Illumina Genome Analyzer is appropriate for generating mammalian draft genome sequences. (genomeweb.com)

Illumina has guidelines about library loading concentration, but these often need optimization. (lu.se)

The NEBNext line of Multiplex Oligos can be used with NEBNext sample prep products or other standard Illumina-compatible library preparation protocols. (neb.com)

News of the Illumina vulnerability comes after the FDA last month announced it will require medical device makers to meet specific cybersecurity requirements when submitting an application for a new product. (yahoo.com)

In a LinkedIn post , Illumina CTO Alex Aravanis said that the company discovered the vulnerability as part of routine efforts to assess its software for potential vulnerabilities and exposures. (yahoo.com)
If the Commission finds that Illumina breached the rule as part of this latest probe, the company could be fined up to 10% of its revenue. (medtechdive.com)
BioMed Realty Trust , a real estate investment company focused on the life sciences industries, said the new facility will expand an existing 110,000-square-foot facility that Illumina leases at the University Towne Center. (sandiegofreepress.org)
As the City Beat article, Mayor Kevin Faulconer's Illumina-ting Pitch stated: "Going forward, will city leaders throw a bone to every company that mentions Texas or some other far-off land of fiscal opportunity? (sandiegofreepress.org)

The NEBNext Multiplex Oligos for Illumina (Unique Dual Index UMI Adaptors RNA Set 1) workflow shown below details the library barcoding steps of the library preparation process. (neb.com)
If library preparation kit is not manufactured by Illumina, please check with the kit producer. (lu.se)

Anatomy5

Organisms10

Diseases1

Chemicals and Drugs10

Analytical, Diagnostic and Therapeutic Techniques and Equipment28

Phenomena and Processes53

Disciplines and Occupations6

Technology, Industry, Agriculture2

Information Science14

Named Groups1

Health Care7

Oxford nanopore2

Sequencing27

MiSeq3

Sequence8

Genomics4

20215

Sequencers2

20233

Illumina's4

FASTQ2

Company's1

Grail16

Expects1

Shareholders2

Genomes2

20241

Galleri1

Accelerator3

Genomic data1

Pacbio4

Roche5

GenomeWeb1

Nicklas Nordborg1

DeSouza1

Adapter1

Algorithms2

Diego4

Shotgun1

Collaboration1

Libraries1

Data4

Researchers1

Dominant1

Regulators1

Begingroup1

Contigs4

Platform1

Capability1

Genome assembly1

Cancer1

Configurations1

Billion1

Transcripts1

Long1

Market1

Million2

Short-read1

Optimization1

Products1

News1

Company4

Library preparation2