New open-source algorithm produces phased diploid genome assemblies
Seattle-based Phase Genomics [www.phasegenomics.com], the leader in Hi-C based genomic solutions and Pacific Biosciences of California, Inc. [www.pacb.com], the leader in long-read sequencing, announce the release of the FALCON-Phase software as part of a new co-development effort to improve the FALCON-Unzip genome assembly method for providing high-quality, phased diploid genome assemblies.
FALCON-Phase augments PacBio® Single Molecule, Real-Time (SMRT®) Sequencing-based assemblies with Hi-C proximity-ligation data to generate accurate phased diploid assemblies. Using Phase Genomics’ genome scaffolding technologies and FALCON-Phase, maternal and paternal haplotypes can be separated or “phased” on a chromosomal scale.
“You essentially get two genomes for the price of one with the FALCON-Phase software yielding both maternal and paternal haplotypes,” said Dr. Ivan Liachko, CEO and Co-founder of Phase Genomics, “The combination of SMRT Sequencing and long-range genomic contiguity captured by Hi-C data is very powerful and presents a straightforward solution to a problem experienced by almost all genomic researchers working with diploid organisms.”
High-quality phased haplotypes provided by FALCON-Phase can, among many other use cases, facilitate the study of inherited disease and be leveraged to improve agricultural programs, such as increasing the efficacy of livestock and plant breeding.
“SMRT Sequencing produces the most accurate and contiguous genome assemblies on the market, and the ultra-long range genomic connectivity of the in vivo Hi-C method serves as a perfect complement to SMRT Sequencing of large and complex genomes, helping to achieve full chromosome-level contiguity and phasing,” stated Dr. Jonas Korlach, Chief Scientific Officer at Pacific Biosciences. “Our collaboration with Phase Genomics has been truly synergistic and has yielded a method that enables researchers to get more value from long-read SMRT Sequencing and Hi-C technologies alone.”
FALCON-Phase is available as open source to scientists and also as a service through Phase Genomics. Scientists can utilize the new software to advance their current research and even revive historic genome projects with the addition of Hi-C data.
Read more about the innovative technology underpinning the new FALCON-Phase software here.
ABOUT PHASE GENOMICS – Phase Genomics applies Hi-C and other proximity-ligation methods to enable chromosome-scale genome assembly, metagenomic deconvolution, as well as analysis of structural genomic variation and genome architecture. They offer a comprehensive portfolio of laboratory and computational services and products, including Hi-C kits for plants, animals, microbes, and human samples as well as industry-leading genome and metagenome assembly and analysis software. Based in Seattle, WA, the company was founded in 2015 by a team of genome scientists, software engineers, and entrepreneurs. The company’s mission is to empower scientists with genomic tools that accelerate breakthrough discoveries.
FORWARD-LOOKING STATEMENTS – All statements in this press release that are not historical are forward-looking statements, including, among other things, statements relating to legal proceedings to enforce patent rights, the validity or enforceability of patents or other intellectual property rights, future availability, uses, quality or performance of, or benefits of using, products or technologies, and other future events. You should not place undue reliance on forward-looking statements because they involve known and unknown risks, uncertainties, changes in circumstances and other factors that are, in some cases, beyond Pacific Biosciences’ control and could cause actual results to differ materially from the information expressed or implied by forward-looking statements made in this press release. Factors that could materially affect actual results can be found in Pacific Biosciences’ most recent filings with the Securities and Exchange Commission, including Pacific Biosciences’ most recent reports on Forms 8-K, 10-K and 10-Q, and include those listed under the caption “Risk Factors.”
Pacific Biosciences undertakes no obligation to revise or update information in this press release to reflect events or circumstances in the future, even if new information becomes available.
Sunak to use budget to expand apprenticeships in England
LONDON (Reuters) – British finance minister Rishi Sunak will announce more funding for apprenticeships in England when he unveils his budget next week, the government said on Friday.
Employers taking part in the Apprenticeship Initiative Scheme will from April 1 receive 3,000 pounds ($4,179) for each apprentice hired, regardless of age – an increase on current grants of between 1,500 and 2,000 pounds depending on age.
The scheme will extended by six months until the end of September, the finance ministry said.
Sunak will also announce an extra 126 million pounds for traineeships for up to 43,000 placements.
Sunak’s March 3 budget will likely include a new round of spending to prop up the economy during what he hopes will be the last phase of lockdown, but he will also probably signal tax rises ahead to plug the huge hole in the public finances.
Sunak is also expected to announce a “flexi-job” apprenticeship scheme, whereby apprentices can join an agency and work for multiple employers in one sector, the finance ministry said.
“We know there’s more to do and it’s vital this continues throughout the next stage of our recovery, which is why I’m boosting support for these programmes, helping jobseekers and employers alike,” Sunak said in a statement.
(Reporting by Andy Bruce, editing by David Milliken)
UK seeks G7 consensus on digital competition after Facebook blackout
LONDON (Reuters) – Britain is seeking to build a consensus among G7 nations on how to stop large technology companies exploiting their dominance, warning that there can be no repeat of Facebook’s one-week media blackout in Australia.
Facebook’s row with the Australian government over payment for local news, although now resolved, has increased international focus on the power wielded by tech corporations.
“We will hold these companies to account and bridge the gap between what they say they do and what happens in practice,” Britain’s digital minister Oliver Dowden said on Friday.
“We will prevent these firms from exploiting their dominance to the detriment of people and the businesses that rely on them.”
Dowden said recent events had strengthened his view that digital markets did not currently function properly.
He spoke after a meeting with Facebook’s Vice-President for Global Affairs, Nick Clegg, a former British deputy prime minister.
“I put these concerns to Facebook and set out our interest in levelling the playing field to enable proper commercial relationships to be formed. We must avoid such nuclear options being taken again,” Dowden said in a statement.
Facebook said in a statement that the call had been constructive, and that it had already struck commercial deals with most major publishers in Britain.
“Nick strongly agreed with the Secretary of Stateâ€™s (Dowden’s) assertion that the governmentâ€™s general preference is for companies to enter freely into proper commercial relationships with each other,” a Facebook spokesman said.
Britain will host a meeting of G7 leaders in June.
It is seeking to build consensus there for coordinated action toward “promoting competitive, innovative digital markets while protecting the free speech and journalism that underpin our democracy and precious liberties,” Dowden said.
The G7 comprises the United States, Japan, Britain, Germany, France, Italy and Canada, but Australia has also been invited.
Britain is working on a new competition regime aimed at giving consumers more control over their data, and introducing legislation that could regulate social media platforms to prevent the spread of illegal or extremist content and bullying.
(Reporting by William James; Editing by Gareth Jones and John Stonestreet)
Britain to offer fast-track visas to bolster fintechs after Brexit
By Huw Jones
LONDON (Reuters) – Britain said on Friday it would offer a fast-track visa scheme for jobs at high-growth companies after a government-backed review warned that financial technology firms will struggle with Brexit and tougher competition for global talent.
Finance minister Rishi Sunak said that now Britain has left the European Union, it wants to make sure its immigration system helps businesses attract the best hires.
“This new fast-track scale-up stream will make it easier for fintech firms to recruit innovators and job creators, who will help them grow,” Sunak said in a statement.
Over 40% of fintech staff in Britain come from overseas, and the new visa scheme, open to migrants with job offers at high-growth firms that are scaling up, will start in March 2022.
Brexit cut fintechs’ access to the EU single market and made it far harder to employ staff from the bloc, leaving Britain less attractive for the industry.
The review published on Friday and headed by Ron Kalifa, former CEO of payments fintech Worldpay, set out a “strategy and delivery model” that also includes a new 1 billion pound ($1.39 billion) start-up fund.
“It’s about underpinning financial services and our place in the world, and bringing innovation into mainstream banking,” Kalifa told Reuters.
Britain has a 10% share of the global fintech market, generating 11 billion pounds ($15.6 billion) in revenue.
The review said Brexit, heavy investment in fintech by Australia, Canada and Singapore, and the need to be nimbler as COVID-19 accelerates digitalisation of finance, all mean the sector’s future in Britain is not assured.
It also recommends more flexible listing rules for fintechs to catch up with New York.
“We recognise the need to make the UK attractive a more attractive location for IPOs,” said Britain’s financial services minister John Glen, adding that a separate review on listings rules would be published shortly.
“Those findings, along with Ron’s report today, should provide an excellent evidence base for further reform.”
Britain pioneered “sandboxes” to allow fintechs to test products on real consumers under supervision, and the review says regulators should move to the next stage and set up “scale-boxes” to help fintechs navigate red tape to grow.
“It’s a question of knowing who to call when there’s a problem,” said Kay Swinburne, vice chair of financial services at consultants KPMG and a contributor to the review.
A UK fintech wanting to serve EU clients would have to open a hub in the bloc, an expensive undertaking for a start-up.
“Leaving the EU and access to the single market going away is a big deal, so the UK has to do something significant to make fintechs stay here,” Swinburne said.
The review seeks to join the dots on fintech policy across government departments and regulators, and marshal private sector efforts under a new Centre for Finance, Innovation and Technology (CFIT).
“There is no framework but bits of individual policies, and nowhere does it come together,” said Rachel Kent, a lawyer at Hogan Lovells and contributor to the review.
($1 = 0.7064 pounds)
(Reporting by Huw Jones; editing by Jane Merriman and John Stonestreet)
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