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...
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
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...
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
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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Command-line interface, or CLI in brief, specifies how a user interacts with a program on the command line. Torsten Seemann wrote a good article on creating CLI. This blog post adds a few more suggestions. 1. Keep the backward compatibility of CLI as much as possible Backward compatibility here means users can upgrade and run a tool without changing the command lines they used in the past. This implies we should not remove or change the meaning of an existing …
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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 couple of weeks ago I sat down for coffee with a pair of MGI representatives - American Region CEO Yongwei Zhang and Director, Global Business Development Damon Zhang. Since I hadn’t been at AGBT 2022 (my 2023 application already filed!). Yongwei and I had planned to try to catch up the next time he was in Boston area, so I braved our current subway issues (not one, but two major lines shut for extended maintenance!) and covered a range …
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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
This was once a guest post by Karol Estrada, who was a postdoctoral research fellow in the Analytic and Translational Research Unit at Massachusetts General Hospital and the Broad Institute of MIT and Harvard. It was written in memory of Laura Riba. We have briefly summarised her thoughts and findings from that post below. Karol … A Rare Variant in Mexico with Far-reaching Implications Read More »
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The common notion running through molecular biology is that the information present in DNA is transferred to RNA and then to protein. Back in 2010, researchers made a potentially ground-breaking observation. They found that within any given individual, there are tens of thousands of places where transcribed RNA does not match the template … Notes on the Evidence for Extensive RNA Editing in Humans Read More »
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In May 2019, it was reported in an article that over ten thousand sequence mismatches were observed between messenger RNA and DNA from the same individuals. More recently, three technical comments were published by Science surrounding this article. It was concluded that at least 90% of the Li et al. RDD sites are technical artifacts. … Questioning the Evidence for Non-Canonical RNA Editing in Humans Read More »
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A little while back, Razib Khan used data from 23andMe to explore his family’s genetic history. He previously published his findings and summarized them. Today, I’m going to fill you in on what he had to say! Khan was interested in genetics, anthropology, and history, mainly how we have changed the way lineages are marked … My Personal Genome: What Razib Khan Had to Say Read More »
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Alzheimer’s disease is a form of dementia that impacts the brain and results in memory loss. In recent years we have been able to study it and its risk factors to calculate the chances of you being affected by the disease. Today we are going to look at how that risk is calculated. Most people … Calculating your Alzheimer’s Risk Read More »
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At the annual Advances in Genome Biology and Technology (AGBT) conference held in Florida during 2012, there were many exciting announcements and developments in the world of DNA sequencing technology. An especially cool piece of news came from the team at Oxford Nanopore, the stars of our piece on cluster sequencing, about their (then) brand … Making Sequencing Simpler With Nanopores Read More »
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Biostar Herald
Share bioinformatics resources from across the web.
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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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