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J.P. Morgan: PacBio

written 2 days ago by Omics! Omics! by Keith Robinson

PacBio CEO Christian Henry’s presentation at J.P. Morgan wasn't rich in technical specifics. But he gave a very bullish portrait of a company aiming for the stars. A conflict reminder: he’s a member of the Board of the Strain Factory that employs me, though I haven’t yet had the pleasure of meeting him.The biggest news is a broad partnership with Invitae four clinical human genome sequencing. The only specific here is that this is not the whole enchilada; platform development will take place both within the Invitae collaboration and outside it. What might that development be?Between Henry’s comments in the Q&amp;A and a few info crumbs on slides there will be pushed to further tune all the canister. Her mentioned efforts on dyes and further improving SMRTcell loading efficiency. There was chatter on Twitter about an overdue update to improve HiFi yields.Henry talked of the importance of increasing ZMW packing, but gave no specifics other than to suggest this is more "development" than "innovation" -- this was in response to a question asking if technical breakthroughs are required. But we are left wondering on a timetable as well as what the next density might be; four-fold to 32M wouldn’t be surprising on naïve geometry grounds. I suspect a huge area of joint effort with Invitae will be to automate HiFi library production. The current protocol is long, manual and labor intensive - not at all appealing for lease scale clinical use. How much of that will be retained as proprietary ...

J.P. Morgan: 10X Genomics

written 5 days ago by Omics! Omics! by Keith Robinson

As I attempt to collate various incomplete thoughts about the J.P. Morgan presentations I have read and listened to from genomics instrument shops, one thing stands out about 10X Genomics: they actually announced new gadgets and kits! I should thank the company for supplying the slides after I snarked on Twitter about how they weren't archived in the J.P. Morgan webcast -- but now it is there. So either my eyes failed again or I had a personal IT failure (I think the website doesn't like iOS and I may have forgotten that). The slides were presented by CEO Serge SaxonovRead more »

NCBI on YouTube: RAPT and BLAST+ on the Cloud, SARS-CoV-2 genome data in Datasets

written 6 days ago by NCBI Insights

It’s time we do another roundup of what’s been happening on YouTube! First up, the NCBI YouTube channel has merged with the NLM YouTube channel. You’ll now be able to find diverse content all on one channel, from tips on using resources to fascinating moments in the history of medicine and more! Use RAPT, the … Continue reading NCBI on YouTube: RAPT and BLAST+ on the Cloud, SARS-CoV-2 genome data in Datasets →

JP Morgan: Illumina

written 7 days ago by Omics! Omics! by Keith Robinson

Illumina presented at J.P. Morgan on Monday, reminding us that they aren't just a sequencing instrument company but an interlocking set of businesses focused on genomics. CEO Francis deSouza spent much of his time discussing the Grail acquisition and some of the other ways in which Illumina is pushing rapidly to become an essential part of clinical medicine, but there was one slide on future improvements to sequencing technology and a few on the lineup of existing sequencers. Reminder: I'm working off public sources, as during the day we work closely with Illumina and they even sunk some serious cash into my employer last May.Read more »

RefSeq release 204 is now available

written 7 days ago by NCBI Insights

RefSeq release 204 is now available online, from the FTP site and through NCBI’s Entrez programming utilities, E-utilities. This full release incorporates genomic, transcript, and protein data available as of January 4, 2021, and contains 262,714,372 records, including 191,411,721 proteins, 35,353,412 RNAs, and sequences from 106,581 organisms. The release is provided in several directories as a complete dataset … Continue reading RefSeq release 204 is now available →

Prokaryotic representative genomes updated — now over 13 thousand assemblies!

written 9 days ago by NCBI Insights

We have updated the bacterial and archaeal representative genome collection! The current collection contains over 13,000 assemblies selected from the 203,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has increased by 11% since August 2020. We’ve included about 1,400 species for the first time, have used better assemblies for 1,177 species, and … Continue reading Prokaryotic representative genomes updated — now over 13 thousand assemblies! →

J.P. Morgan 2021

written 10 days ago by Omics! Omics! by Keith Robinson

The J.P. Morgan Healthcare Conference has started this morning in virtual form, so I'd really better get this draft cleaned up and out (indeed, Roche is presenting as I hurriedly type, though about pharma not diagnostics). 2021 already feels like a darker continuation of 2020, between the appalling putsch attempt in my nation's center of government last Wednesday and the still buggy roll-out of the coronavirus vaccine. As I noted in my piece on the Oxford Nanopore Community Meeting, the many disruptions of 2020 make grading the progress of companies essentially impossible: many were disrupted by lockdowns, supply chain issues and the general distraction from the year of doomscrolling. Read more »

Job: Bioinformatics Developer

written 10 days ago by Ensembl Blog

We’re seeking a bioinformatician to work on variant annotation and curation tools. We’re looking for an experience of working with genetic variation data, proficiency in at least one programming language and UNIX/Linux environment. Closes 17th February. Location: EMBL-EBI, Hinxton near Cambridge, UK Staff Category: Staff Member Contract Duration: Until the end of March 2022 Grading: […]

Job: Ensembl Variation Project Leader

written 10 days ago by Ensembl Blog

We’re looking for a Project Leader to manage the Ensembl variation and phenotype resources. We’re looking for an in-depth understanding of bioinformatics, genetic variation and genomics, as well as an experience in people management and designing database systems. Closes 31st January. Location: EMBL-EBI, Hinxton near Cambridge, UK Staff Category: Staff Member Contract Duration: 3 years Grading: […]

What coming in release 103

written 14 days ago by Ensembl Blog

We’re planning to release Ensembl 103 in February 2021. We’ve got lots of plans, although we can’t guarantee everything will make it into the release. Mouse The new mouse genome assembly, GRCm39 The mouse strains alignment will be recalculated as EPO using the new assembly. Human Some transcripts will be labelled as MANE Plus Clinical. […]

GenBank release 241.0

written 14 days ago by NCBI Insights

GenBank release 241.0 (12/21/2020) is now available on the NCBI FTP site. This release has 12.98 trillion bases and 2.27 billion records. The current release has 221,467,827 traditional records containing 723,003,822,007 base pairs of sequence data. There are also 1,517,995,689 WGS records containing 11,830,842,428,018 base pairs of sequence data, 446,397,378 bulk-oriented TSA records containing 392,206,975,386 … Continue reading GenBank release 241.0 →

Open: Ensembl Browser and REST API virtual workshops

written 15 days ago by Ensembl Blog

Registration is now open for two free virtual Ensembl workshops covering the genome browser and the REST API. The Browser workshop will be held between Tuesday 26th January – Thursday 28th January 2021 (2pm-5pm) and the REST API workshop will be held between Wednesday 3rd February – Friday 5th February 2021 (2pm-4:15pm). More information and […]

Important Changes to NCBI Accounts Coming in 2021

written 16 days ago by NCBI Insights

Do you login to NCBI to use MyNCBI, SciENcv, or MyBibliography? Do you submit data to NCBI? If so, you’ll want to read further to get a first glimpse at some important changes to NCBI accounts that will be coming in 2021. What’s happening? In brief, NCBI will be transitioning to federated account credentials. NCBI-managed … Continue reading Important Changes to NCBI Accounts Coming in 2021 →

Retrieve genome data by BioProject using the Datasets command-line tool

written 16 days ago by NCBI Insights

You can now retrieve genome data using the NCBI Datasets command-line tool and API by simply providing a BioProject accession. You can go directly from a BioProject accession to genome data even when the BioProject accession is the parent of multiple BioProjects (Figure 1). Figure 1. Command-lines using BioProject accessions with the datasets command-line tool and sample metadata. Top … Continue reading Retrieve genome data by BioProject using the Datasets command-line tool →

Advent of Code vs. FizzBuzz

written 17 days ago by Omics! Omics! by Keith Robinson

A bunch of coding types at the Strain Factory participated in The Advent of Code, a clever 24-day set of programming challenges that runs each year before Christmas. Each day a new two=part programming challenge was posted. Technically it is a speed contest, but you won't find me on the public leaderboard as I'm not nearly quick enough to ever rate a point there. One of my major official activities last month was contributing towards screening candidates for three different computational positions, one of which we threw open to general data science experience. As a result, I've been thinking far too much about the FizzBuzz problem and my prejudices towards it.Read more »

Peri-New Year Nanopore Playing

written 19 days ago by Omics! Omics! by Keith Robinson

Ever since the community meeting I've been toying with an idea, then never quite trying to code it. So on New Year's Eve I started getting the dataset together and reducing it to a bunch of dataframes, and today I pushed that a bit further and started graphing some of it. It's very much a rough project -- some of the dataframes have some issues I'm still chasing down with redundant data not being initially collapsed, but I think the data is accurate. I also think I have my conventions consistent -- at one point confused myself into inverting the labels on the plots! In other words, ApG would be labeled GpA -- not good! There's already some intriguing patterns, which are presumably the sort of signal tools like Medaka use to polish assemblies from FASTQ data aligned to draft references.Read more »

Expanding access to coronavirus-related literature: the COVID-19 Initiative in PMC reaches 100K articles!

written 4 weeks ago by NCBI Insights

One important way the National Library of Medicine (NLM) is responding to the ongoing public health emergency is through the COVID-19 Initiative. This public-private cooperation between NLM and more than 50 scholarly publishers and societies allows you to access over 100,000 articles on COVID-19, SARS-CoV-2 and other coronaviruses through PubMed Central (PMC). This collection includes … Continue reading Expanding access to coronavirus-related literature: the COVID-19 Initiative in PMC reaches 100K articles! →

NCBI hidden Markov models (HMM) release 4.0 now available!

written 4 weeks ago by NCBI Insights

Release 4.0 of the NCBI hidden Markov models (HMM) used by the Prokaryotic Genome Annotation Pipeline (PGAP) is now available from our FTP site. You can search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package. This release contains 17,443 models, including 94 new models since the … Continue reading NCBI hidden Markov models (HMM) release 4.0 now available! →

Nanopore Community Meeting: Progress Despite the Pandemic

written 4 weeks ago by Omics! Omics! by Keith Robinson

I realized a few Oxford Nanopore announcements too late that I should have tried to log all their predictions with a date made so I could track carefully any delays or quiet disappearances from the new feature lineup. If I had done that, this year would have presented an even worse conundrum: how do you score progress in a year of constant disruptions? Like many companies in the sequencing field, at least some of that disruption has been a diversion of attention and resources to fighting the pandemic. For ONT that is largely supporting the ARTIC viral genome sequencing and also developing LamPORE diagnostics.Read more »

The Protein Family Model resource is now available!

written 4 weeks ago by NCBI Insights

The new Protein Family Model resource (Figure 1) provides a way for you to search across the evidence used by the NCBI annotation pipelines to name and classify proteins. You can find protein families by gene symbol, protein function, and many other terms. You have access to related proteins in the family and publications describing … Continue reading The Protein Family Model resource is now available! →

BGI Floats Idea of Tape-Based Sequencer

written 5 weeks ago by Omics! Omics! by Keith Robinson

I reported on the AGBT 2020 final talk a few centuries ago -- or at least it seems like that given how quickly the world went to hell just after that -- by BGI in which Rade Drmanac showed off a system which I described as a deconstructed sequencer -- an integrated set of plate handling robots, liquid handlers and imagers which dipped the slides into reservoirs of reagents instead of flowing them through a flowcell. Now BGI has a preprint on BioRxiv which takes this idea a bit further, changing out the reagent tanks for a polymer film on which a thin layer of reagent is distributed, which is then pressed gently against the slide surface to deliver the reagent to the DNA Nanoball (DNB) array. The preprint is filled with eye-popping numbers -- Petabase sequencing!Read more »

Job: Bioinformatics Developer

written 5 weeks ago by Ensembl Blog

We’re looking for a bioinformatics developer to help expand our comparative genomics resources. We’re looking for a BSc, MSc or equivalent experience in computational biology or bioinformatics and practical experience working with big data. Closes 22nd January. Location: EMBL-EBI, Hinxton near Cambridge, UK Staff Category: Staff Member – Science, research and training Contract Duration: 3 years […]

MANE progress update

written 6 weeks ago by Ensembl Blog

NCBI and EBI have been hard at work on our joint MANE collaboration, aiming to provide a set of representative transcripts for human protein-coding genes that are identically annotated in the NCBI RefSeq and Ensembl/GENCODE annotation sets and exactly match the GRCh38 reference assembly. We released MANE v0.5 in Dec 2018, which included one well-supported […]

Best Genealogy Software

written 7 weeks ago by Genomes Unzipped

Researching your family history is a fascinating experience. Even if you find out that your ancestors led very normal lives. Just being able to see the name and life milestones of your great-great-great-great-great (etc) grandmother is exciting.It’s amazing to be able to track your ancestry. But it can also be a confusing process. This is … Best Genealogy Software Read More »

Best DNA Test for Health

written 7 weeks ago by Genomes Unzipped

These days we can find out virtually anything we want with the swipe of a finger. But what do we know about our health?Yes, we can see our local doctor, but what about our genetic makeup? DNA tests for health show us a range of factors that are influenced by our genetic makeup. These include: Genetic health … Best DNA Test for Health Read More »
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