Category Archives: next generation sequencing

DNA extraction for PacBio sequencing

PacBio is emerging as the favoured sequencing approach for assembling high-quality reference genomes. But the big issue with PacBio sequencing is that to get long sequence reads you need to start with high molecular weight DNA. For my first foray … Continue reading

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Signal Boosting a Comprehensive Review of eDNA and Metabarcoding Studies

Everything is meta these days – metabarcoding, metagenomics, and now meta blog posts that are reviews of reviews. Much like every ecologist at least dabbles in the molecular world, so most of those predisposed to molecular ecology and population genetics … Continue reading

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Posted in bioinformatics, community ecology, DNA barcoding, metagenomics, methods, microbiology, next generation sequencing, population genetics | Tagged , , , , , , , , , , | Leave a comment

Sequencing round-up 2018

The deluge of new sequencing approaches continues at a pace. It seems that you turn your back for five minutes and there’s a shiny new sequencing platform promising to deliver more for less. What is the current state of play … Continue reading

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Major new microbial groups expand diversity and alter our understanding of the tree of life

I still believe in revolutions. And sometimes they just happen, almost unnoticed. One such revolution happened on a boring 11th of April 2016 when Laura Hug et al. published their new tree of life in the journal of Nature Microbiology. … Continue reading

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Posted in bioinformatics, community ecology, evolution, genomics, metagenomics, microbiology, next generation sequencing, phylogenetics | Tagged , , , , , , , | Leave a comment

Retrieving a million sequences and avoiding primer bias, a new method that might have it all

We have come a long way since the early days when sequencing was a breakthrough method initially used to identify uncultured microbes from the environment. It is now been almost three decades, in fact, since the first microbial 16S rRNA … Continue reading

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Molecular ecology, the flowchart

Towards the end of last semester my department’s evolutionary genetics journal club read Rasmus Nielsen’s terrific 2005 review of tests for recent natural selection in genetic data. Nielsen provides figures illustrating the effects of a recent selective sweep and the … Continue reading

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Posted in association genetics, bioinformatics, genomics, howto, infographic, linkage mapping, next generation sequencing, phylogenetics, phylogeography, population genetics, selection | Leave a comment

We have the technology. Is sequencing getting better, smaller, faster?

Okay, I know some version of the phrase “recent developments in rapid and affordable sequencing have made blah blah blah possible…” is something you’ve probably read 10,000 times. However, third-generation sequencing platforms have turned out to be pretty darn astounding. … Continue reading

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Non-model organisms are so hot right now

What makes a model organism? Well, as the name suggests, they are widely studied and have been adapted to a vast array of common genetic techniques. A few of the most often utilized organisms, which you are most likely already … Continue reading

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Posted in bioinformatics, domestication, evolution, genomics, next generation sequencing, yeast | Tagged , | Leave a comment

Genomes are coming: Sequence libraries from the honey bee reflect associated microbial diversity

One of the coolest of reasons that cheap sequencing is nifty, in my opinion, is that it has allowed researchers to study individual eukaryotic organisms, and their associated microbes (their microbiome). Let’s be real, we are in the midst of … Continue reading

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Posted in Coevolution, community ecology, evolution, genomics, metagenomics, microbiology, next generation sequencing | Tagged , , | Leave a comment

Easily aggregate bioinformatic sample output with one tool

Today I’m going to write about one of my favorite bioinformatic tools, MultiQC. If you’ve used it, you know why, and if you haven’t, prepare to be amazed. Many bioinformatic software produce output on a per-sample basis. That is, you … Continue reading

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