Category Archives: genomics

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

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Of microbes and men: Testing the neutral theory with the human microbiome

There is no doubt that one of the hottest current topics in microbiology revolves around the human microbiome. There have been a suite of recent studies we’ve highlighted, on organisms ranging from bees and mice, to humans. A quick google scholar search identifies … Continue reading

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Understanding the pieces of all those meeces: characterizing mice gut microbiota

In an age where a tremendous amount of data is generated, this week has seen some moves towards providing open access to extensive data sets. These attempts have been in the realm of chemistry as well as microbiology, where in a … Continue reading

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On (mis)interpreting STRUCTURE/ADMIXTURE results

STRUCTURE, ADMIXTURE and other similar software are among the most cited programs in modern population genomics. They are algorithms that estimate allele frequencies and admixture proportions under the premise that sampled genotypes are derived from one of “K” ancestral populations, … Continue reading

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The Genomics of Rapid Adaptation

Phenology (the timing of life cycle events such as growth, breeding, or migration) is among the most sensitive organismal traits to climate and environmental change. In recent years, phenological shifts have been documented in numerous taxa, in traits such as … Continue reading

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Molecular Inversion Probes: phylogenomics without the excess?

The onset of the phylogenomic era has revolutionized molecular ecology and systematics, helping resolve relationships throughout the tree of life that have long eluded researchers working with only a handful of loci and morphological data. Phylogenetic studies of nonmodel organisms … Continue reading

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STITCH, in time, could save a lot of array design

A new algorithm for processing DNA sequence data, STITCH, could lower costs for studies of genetic variation within species by reconstructing, or “imputing”, the sequences of individual samples within a larger dataset. The ongoing proliferation of high-throughput (or, ugh, “next … Continue reading

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