Category Archives: next generation sequencing

Spontaneous mutations—friend or foe?

The following is a cross-posting from the Stanford CEHG Blog by Ryo (Ryosuke) Kit, a graduate student in Hunter Fraser’s lab at Stanford University. Evolution has conflicting opinions about spontaneous mutations. Spontaneous mutations produce the genetic variation that drives evolution … Continue reading

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Scanning the genome for local adaptation

One of the most obvious and important applications of evolutionary genetics is in figuring out whether natural biological communities are going to be able to adapt to global climate change. The projected rate of climate change over then next century … Continue reading

Posted in adaptation, association genetics, genomics, next generation sequencing | Tagged , , | 4 Comments

2014 NGS Field Guide: Resistance is Futile (mostly, at least for a while)

This year, to introduce the 2014 update to his Next Generation Sequencing Field Guide—perennially our most-accessed community resource—Travis Glenn has a bit more to say than just what goes in the tables. So here it is as a guest post! … Continue reading

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No reference genome? No problem! Demographic inference from genomic data in nonmodel insect populations

This guest article by Martin Sikora is cross-posted from the Computational, Evolutionary and Human Genomics blog at Stanford University. Reconstructing the demographic history of species and populations is one of the major goals of evolutionary genetics. Inferring the timing and … Continue reading

Posted in genomics, next generation sequencing, population genetics | 2 Comments

Want to share your code?

In this line of work, we have all encountered tasks that are tedious, time consuming, and repetitive.  (Or if not, maybe give it a bit more time.) When confronted with these situations, people tend to fall into one of two … Continue reading

Posted in bioinformatics, community, genomics, howto, methods, next generation sequencing, phylogenetics, population genetics, quantitative genetics, R, software, theory | 14 Comments

Phylogeny-aware comparisons of microbial communities – EdgePCA and Squash Clustering

I’m jumping on the bandwagon with a blog post about this new PLoS ONE paper (taking the lead from the man in charge in my lab) because the algorithms are just so exciting: Matsen FA IV, Evans SN. (2013) Edge Principal … Continue reading

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Q&A: Yannick Wurm wrangles RADseq to learn why some fire ants bow to more than one queen

Yannick Wurm grew up in Redwood City, California, and his initial plan was to design interfaces for Apple. But he went to university at the Institut National des Sciences Appliquées in Lyon—where, after two years of general engineering courses, the … Continue reading

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Next-gen sequencing field guide, 2013 edition

Travis Glenn has updated his Field Guide to Next-Generation Sequencing, originally published in 2011, to account for changes to this almost axiomatically dynamic field. The 2013 update to the Field Guide tables is online here. Previous editions of the tables … Continue reading

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STACKS: A program for identifying and genotyping loci with next-generation sequencing data

If you have recently collected or are in the process of collecting next-generation sequencing data, then you may be wondering what the next step to working with your data will entail.  Hopefully, you have been working a little bit with … Continue reading

Posted in methods, next generation sequencing, population genetics, software | Tagged , , | 1 Comment

A comparison of bioinformatics programming languages

The times are a-changin and most molecular ecologists and evolutionary biologists are no longer asking themselves, “Should I learn a programming language?”, but rather “Which programming language should I learn?”. There are a variety of programming languages that are used by … Continue reading

Posted in bioinformatics, next generation sequencing, software | 10 Comments