Welcome to the Sequencing 101 blog series – where we will provide introductions to sequencing technology, genomics, and much more! If you’re not immersed in the field of DNA sequencing, it can be challenging to keep up with the rapid evolution among all the platforms and technologies on the market. Let’s start with a quick overview of how these different technologies came about — and how each is used today. The evolution of sequencing technology. First Generation Sequencing – Starting the Era of Genomics The process of Sanger sequencing. DNA sequencing as we know it originated in the late…
Hundreds of SMRT scientists came together recently in Leiden to learn about the latest updates to PacBio technology and to showcase their data analysis tools. Extremely useful information was shared, and future collaborations were sparked. For those who weren’t able to jet to the Netherlands to attend, we’ve rounded up the top tools and tips presented at the European SMRT Informatics Developers Meeting. For an in-depth report on the event, check out this blog post by PacBio Principal Scientist Elizabeth Tseng. SMRT Link – Of course our own open-source SMRT analysis software suite will be top of the list. Updates…
We’re thrilled to announce the launch of the Sequel II System, reducing project costs and timelines with approximately eight times the data output compared to the previous Sequel System. It enables customers to comprehensively detect human variants ranging in size from single nucleotide changes to large, complex structural variants. The system is also ideal for standard applications such as de novo assembly of large genomes and whole transcriptome analysis using the Iso-Seq method. The Sequel II System is based on the proven technology and workflow underlying the previous version of the system, but contains updated hardware to process the new…
Today we’re pleased to announce the release of Sequel System 6.0, including new software, consumable reagents and a new SMRT Cell. Combined, the enhancements in the release improve the performance and affordability of Single Molecule, Real-Time (SMRT) Sequencing by providing individual long reads with greater than 99% accuracy, increasing the throughput up to 50 Gb per SMRT Cell, and delivering average read lengths up to 100,000 base pairs, depending on insert size. These improvements are expected to greatly enhance the accuracy and cost effectiveness of applications such as whole genome sequencing, human structural variant detection, targeted sequencing and RNA transcript isoform sequencing (Iso-Seq method). Estimated…
UPDATED Dec. 3, 2018 Congratulations to the Italian team on the publication of their European barn swallow genome! The paper is now available at GigaScience. ORIGINAL POST Oct. 3, 2018 With its bold blue plumage, russet throat and chipper chirps, the barn swallow is beloved by many avian enthusiasts. It’s also a favorite of scientists, becoming a flagship species for conservation biology. Numerous evolutionary and ecological studies have focused on its biology, life history, sexual selection, response to climate change, and the divergence between its eight subspecies in Europe, Asia and North America. But the full potential of such studies has…
Structural variants account for most of the base pairs that differ between human genomes, and are known to cause more than 1,000 genetic disorders, including ALS, schizophrenia, and hereditary cancer. Yet they remain overlooked in human genetic research studies due to inherent challenges of short-read sequencing methods to resolve complex variants, which often involve repetitive DNA. At a recent webinar co-hosted by Nature Research, Professor Alexander Hoischen joined Principal Scientist Aaron Wenger to discuss how advances in long-read sequencing and structural variant calling algorithms have made it possible to affordably detect the more than 20,000 such variants that are…
Pop quiz: Which animal accounts for around 20% of all living mammals, harbors (yet survives) some of the world’s deadliest diseases, lives proportionately longer than humans given its body size, and helps make tequila possible? Answer: Bats. From the tiniest bumblebee bat (Craseonycteris thonglongyai) to the large (1kg) golden-capped fruitbat (Acerodon jubatus), the diversity and rare adaptations in bats have both fascinated and terrified people for centuries. Now, an international consortium of bat biologists, computational scientists, conservation organizations, and genome technologists has set out to decode the genomes of all 1,300 species of bats using SMRT Sequencing and other technologies.…
From wild animals to perfect pets, dogs have undergone some interesting changes during their centuries-long domestication. Intent on unraveling some of the developmental secrets of the process, a team of scientists from the University of New South Wales in Sydney, Australia, is doing deep dives into the genomes of a range of canine cousins along the evolutionary chain. A desert dingo named Sandy has already provided some insight into the process after its genome was sequenced as part of the 2017 Plant and Animal SMRT Grant. Study leader Bill Ballard described in this presentation at PAG 2018 that pure dingoes…
Aspergillus ochraceus The Department of Energy has its eyes on an unassuming solution to our bioenergy needs: Aspergillus. The fungal genus contains hundreds of variations, which include powerful pathogens, industrial cell factories, and prolific producers of bioactive secondary metabolites. The DOE’s Joint Genome Institute (JGI) has embarked on an ambitious plan to sequence, annotate and analyze the genomes of 300 Aspergillus fungi, and the first results are in. In a study published in the Proceedings of the National Academy of Sciences, “Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species,” a team led by researchers at…
A new review in Nucleic Acids Research offers a sweeping look at human sequencing applications for SMRT Sequencing, finding that “[t]he myth that SMRT sequencing is too error prone … is being expunged and replaced by evidence that it offers advantages over short-read sequencers.” The authors conclude with a prediction about the ultimate potential for SMRT Sequencing and other “third-generation” platforms: “Just as second-generation platforms stepped beyond Sanger sequencing and enabled a revolution in genomics medicine, third-generation single molecule sequencing platforms will likely be the next genetic diagnostic revolution.” “Single molecule real-time (SMRT) sequencing comes of age: applications and utilities…
A project that sparked widespread interest and a successful science crowdsourcing campaign has inspired an international collaboration that produced two high-quality reference genomes, as well as a draft genome of a related beetle. And the results have shed light on the evolution of bioluminescence. We’ve been following the progress of Team Firefly since the team of scientists from MIT, University of Rochester, Brigham Young University, Indiana University, Cornell University, and Tufts University narrowly lost our 2016 SMRT Grant competition. The project to sequence the genome of the Big Dipper Firefly, Photinus pyralis, was ultimately crowdfunded through the Experiment site and…