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Tag Archives: RADseq
To RADseq or not to RADseq?
It’s a cliche to say that we live in a moment of unprecedented possibility for molecular ecology, as high-throughput sequencing methods drive the cost of collecting DNA sequence data ever lower. But at the same time, it’s a tricky moment, … Continue reading
The trouble with PCR duplicates
The sequencing center just sent your lane of Illumina data. You’re excited. Life is great. You begin to process the data. You align the data. You check for PCR duplicates. 50 percent. Half of your data is garbage. Everything is … Continue reading
Posted in bioinformatics, genomics, methods, next generation sequencing
Tagged genomics, methods, PCR duplicates, RADseq
6 Comments
RADseq and missing data: some considerations
Unlike Sanger sequencing, where loci are directly targeted for each individual and sequencing errors are relatively rare, massively multilocus datasets from next generation sequencing platforms are characterized by large amounts of missing data. This is particularly true for restriction digest … Continue reading
hyRAD and museum genomics
While the RAPTURE may have arrived, the development of novel restriction digest-based library prepartation techniques — and portmanteaus — continues unabated. In a paper published in PLoS ONE last month (and previously available as a preprint on bioRxiv), Tomasz Suchan … Continue reading
RADseq vs. UCEs, round 3
Though reduced-representation genome sequencing (or high-throughput, or nextgen, or massively parallel sequencing, or…) has become standard practice for molecular ecology labs over the past few years, the relative merits of different library preparation methods remains an active area of research. … Continue reading
Posted in bioinformatics, evolution, genomics, methods, next generation sequencing, phylogenetics
Tagged Piranga, RADseq, UCE, ultraconserved elements
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The 2016 Workshop on Genomics summary
I recently had the pleasure to spend two and a half weeks in the beautiful medieval town of Český Krumlov, Czech Republic. The reason was the popular Workshop on Genomics that was running and I was one of the TAs … Continue reading
Posted in bioinformatics, genomics, next generation sequencing
Tagged bioinformatics, genomics, NGS, RADseq, RNAseq, unix, workshop
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Earthquakes and rapid evolution
The 1964 Alaskan earthquake was landscape-altering in creating/uplifting numerous islands in the Gulf of Alaska, providing an ideal system to study adaptive evolution of diversification in affected species – the threespine stickleback (Gasterosteus aculeatus) being a widely studied example. In … Continue reading
Comparing your options for phylogenomic data
The choices for current-generation (last generation?) molecular markers are grouped in two primary camps. First, the “reduced representation” methods: take some DNA, cut it up with specific enzymes, tag those pieces, read the sequences. These methods produce lots and lots of … Continue reading
Posted in methods, next generation sequencing, phylogenetics
Tagged phylogenomics, RADseq, UCE
2 Comments
Isolation by Aesop’s Fable in NYC mice
The story goes like this: Town Mouse goes to visit his friend in the country. Town Mouse looks down his long nose at the food offered by Country Mouse, so he brings Country Mouse back to the city for a … Continue reading
Genetic distance predicts the spread of deadly fungal infections in bats
You’ve probably heard about White-Nose Syndrome (WNS), the particularly nasty fungal pathogen that has decimated North American bat populations over the last decade. Not only has WNS been extremely deadly, but the speed at which it’s spread has been alarming. Really alarming: Understanding … Continue reading
Posted in Molecular Ecology, the journal, phylogeography, population genetics
Tagged pathogens, RADseq
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