Long-read sequencing enables the phasing of variants and reads, i.e., separating those into two parental haplotypes. Without trio information, you will not be able to say which variant is inherited from which parent, but you will know which variants were inherited together. And this matters, e.g., for compound heterozygous variants and cis-regulatory variation. Phasing can… Continue reading Announcing Phasius for visualization of phase blocks
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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One of the most ridiculous and inadvertently hilarious genres in nonfiction is the “five-year plan.” I became acquainted with this literary form in my first grade in Communist Romania. At the end of the year, I stood in front of an audience of teachers, parents, and party bosses and read aloud the following immortal sentence: “We, the proletariat, pledge to fulfill the five-year plan in four years.” The local communist bosses seemed pleased with my reading of their text. It …
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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Of course, having a newer version of the nanopore base caller will have some impact. The accuracy obviously constantly improves, and in long-running projects like ours, we now have samples with Guppy4, Guppy 5, and Guppy 6 base caller versions.I reasoned that it would probably be a confounder, but we mainly look at structural variation.… Continue reading Beware of confounding basecaller versions
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Rare genetic diseases were one of the first beneficiaries of the high-throughput sequencing revolution. Gene discovery in rare disease was once a laborious endeavor that required gene mapping approaches — linkage analysis in dominant pedigrees, or homozygosity mapping in consanguineous families — to narrow the search space, followed by targeted sequencing of coding regions of […] The post A Decade of Gene Discovery in Rare Disease appeared first on KidsGenomics.
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
go to blog
The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
go to blog
The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
go to blog
The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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Periodically in my work or during writing this blog I come across computational problems that have the aspects of making, at least in my mind, very good teaching problems. Some of the characteristics are that the basic problem is relatively simple to explain, the skills required are reusable on other problems, the concepts are germane to other problems and that the posed problem can be expanded in steps to something much richer. Such problems might even be the nucleus of …
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PacBio has been rolling out announcements around the ASHG meeting and now delivers a huge one: the next generation SMRT instrument “Revio” will roll out next spring and it’s a big step up in throughput. With Revio’s 15X boost in per-run throughput over Sequel IIe, PacBio is touting this as 30X HIFi genomes for under $1K sequencing consumables per genome. Read more »
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I am releasing Cramino today, my first Rust experience. Cramino is a faster replacement for NanoStat, and extracts features from cram and bam files that are useful for quality assessment of long read sequencing data, including read lengths and read identities. The default output looks like below (left), and is generated in 12 minutes for… Continue reading Introducing Cramino: a *fast* QC tool
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I have a new hobby: camera traps, also known as trail cameras. Strapped to trees in my local bushland they sit in wait, firing automatically when triggered by a passing animal. Once in a while, something quite magical happens. The camera model I chose is the Campark T85 which for me, had the right combination … Continue reading Editing metadata in trail camera images using R, magick and exiftool
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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A $k$-long sequence $P$ is a ($k$,$s$)-open-syncmer, $s\le k$, if $P[1,s]$ is the smallest among all $s$-mers in $P$. Suppose function $\phi$ is a bijective hash function of $k$-long sequences. $P$ is a random ($k$,$s$)-syncmer if $\phi(P)$ is an open syncmer. Because we often map $k$-mers to integers, $\phi$ can take the form of an invertible integer hash function. In practice, $\phi$ does not have to be a bijection. It can also map a sequence to an integer of a …
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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A week ago, a company calling itself General Inception emerged from stealth as a new concept, which they call an “Igniter company”, to promote the formation of new life sciences company. As described to me in a phone conversation with General Inception CEO Paul Conley, General Inception provides a range of science and business expertise and support to enable embryonic ideas to condense into functional startups. The igniter metaphor Conley offered me is the spark plug of a car: it …
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The Only Thing Clear About Infinity Is It Is Now Complete Long Reads. Illumina told us a new name for Infinity -- Illumina Complete Long Reads -- and an initial pair of products, but didn't reveal anything new about the underlying tech. They threw out a number of claims, but very vague ones. Particularly confusing is that it "isn't synthetic reads". If not, then what is it? Read more »
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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Biostar Herald
Share bioinformatics resources from across the web.
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Dan Graur is the author of the book Molecular and Genome Evolution (2016). Dan Graur has a very low threshold for hooey, hype, hypocrisy, postmodernism, bad statistics, ignorance of population genetics and evolutionary biology, and hatred of any kind. This blog is a diary of peeves, dislikes, antipathies, annoyances, and random feelings of contempt. Rarely, do I have good things to say.
Following a silly letter from Scotland, I found it necessary to state very, very clearly that all the opinions expressed in this blog are my own and do not represent the views of either my academic employer or the current Secretary of the Flat Earth Society.
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