Category Archives: methods

The road ahead

It’s been almost two weeks since we woke up to the reality that Donald Trump — the failed casino mogul, the virtuoso tax-dodger, the reality-show star, the self-described serial sexual assailant, the Ku Klux Klan endorsee and darling of white … Continue reading

Posted in citizen science, community, funding, NIH, NSF, politics, United States | 3 Comments

Divergence and Linked Background Selection

We have widely discussed the reduction in neutral diversity due to demography and linked selection effects (e.g. selective sweeps and hitchhiking, or background selection) in several previous posts (e.g see here, here, and here). However, how linked selection affects neutral divergence … Continue reading

Posted in evolution, genomics, methods, selection, speciation, theory | Tagged , , , , , | Leave a comment

The almighty CRISPR-Cas9 technology: The future of conservation?

In the first post on CRISPR-Cas9, I’ve explained how bacteria and archaea create a “database” of infections and use it as a form of prokaryotic immunization. This time, I’m going to concentrate on how biotechnology turns this natural phenomenon into … Continue reading

Posted in conservation, evolution, methods, theory | Tagged , , , | 1 Comment

When your programming may be inadequate to the task: new options for metagenome analysis

There’s a lot of data in the form of metagenomes out there, and picking apart those mountains of data to uncover meaningful results is difficult. Recently, we received a suggestion from a reader to discuss a recent program (CLARK-S) developed … Continue reading

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The almighty CRISPR-Cas9 technology: How does it work?

CRISPR-Cas9 took the whole world of biology by storm. Selected Science’s 2015 Breakthrough of the Year, the CRISPR-Cas9 technology is revolutionizing science. Within five years of the official announcement (Jinek et al. 2012), it became the genome-editing technique of choice. … Continue reading

Posted in evolution, genomics, methods, theory | Tagged , , , | 1 Comment

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 , , , | 3 Comments

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

Posted in bioinformatics, genomics, howto, methods, population genetics, software, STRUCTURE | Tagged , , , , | Leave a comment