trout: finding tandem repeat outliers in a cohort
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Getting locked in
<p>Like many people who work in bioinformatics, my background was in biology and had nothing to do with computers. As I worked longer in this field, my responsibilities grew from writing code and perf...
aSTRonaut, now in Rust
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E.coli Doesn't Like Diets Either, At Least Genomic Ones
Another interesting preprint that fits several recent themes - genome minimization, discontinuation of products - comes from <a href="https://www.biorxiv.org/content/10.64898/2026.06.01.729178v1">a Ja...
Shredding Genomes: Establishing Plausible Deletability
There's an <a href="https://www.biorxiv.org/content/10.64898/2026.05.29.728882v1">interesting new preprint from Jay Shendure's lab</a> which introduces the technique of Shred-Seq, which is a Cas3-driv...
Dorado v2.0.0 part 2: assembly polishing
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Dorado v2.0.0: no more sup?
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Is Truth Absolutely Necessary for Science?
<p>These days, corporate entities are increasingly dominating research in basic science. This essay looks into how this will change the most cherised convention of science.</p> <!--more--> <p>Resear...
Batch Effect: To Correct or Not for Bulk RNA-seq Data
<p>A colleague sent me a PCA plot last week. Three replicates per condition, control vs KO of a gene. PC1 cleanly separated replicate 1 from replicate 2 from replicate 3. PC2 separated control vs KO. ...
Pawsitively prehistoric
First described from Laos in 2005, the Laotian rock rat Laonastes aenigmamus quickly gained fame as one of the most remarkable “living fossil” discoveries in modern mammalogy. A. Abramov (Zoological I...