Category Archives: methods

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

Posted on 15 Jan, 2013 by Mark Christie

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 , , | 3 Comments

Molecular Ecology Online Forum, 2012

Posted on 24 Oct, 2012 by Jeremy Yoder

Welcome to the Molecular Ecologist Online Forum, which brings together panelists from the Molecular Ecologist Symposium at the Ottawa 2012 Joint Congress on Evolutionary Biology to continue that meeting’s fruitful discussion. (Video and slides from that symposium are available online … Continue reading →

Posted in conferences, methods, next generation sequencing, population genetics | 3 Comments

Dramatically reducing sequencing error via Duplex Tag sequencing

Posted on 2 Oct, 2012 by hollybik

An exciting new study was published in PNAS last month, an open access paper entitled “Detection of ultra-rare mutations by next-generation sequencing”. This new method has the potential to open up a new frontier in Next-gen sequencing bioinformatics, since it allows … Continue reading →

Posted in methods, next generation sequencing | Tagged , , , , | 5 Comments

Isolating isolation by distance

Posted on 4 Sep, 2012 by Jeremy Yoder

Update, 29 Jan 2015: This post has been edited to remove a video clip from the movie “Chinatown,” which was jarring and really just unnecessary, as pointed out in the comments. At its most basic level, population genetics is about … Continue reading →

Posted in methods, population genetics | Tagged , , , , | 12 Comments

Calculating pair-wise, unbiased Fst with R:

Posted on 14 May, 2012 by Mark Christie

Calculating Weir and Cockerham’s FST is very useful because it is unbiased with respect to sample size (Weir and Cockerham 1984).  Without adjusting allele frequency estimates with respect to sample sizes, estimates of FST can be upwardly biased (see Waples … Continue reading →

Posted in methods, population genetics, software | 16 Comments

A penny for your method: Rohland and Reich (2012)

Posted on 28 Jan, 2012 by Jeremy Yoder

This post, which discussed results published by Rohland and Reich (2012), has been removed at the request of Beckman Coulter legal counsel.

Posted in howto, methods, next generation sequencing | 4 Comments

A penny for your method: Nutator

Posted on 2 Dec, 2011 by Brant Faircloth

This one requires a little ingenuity on your part (and perhaps some craft, duct tape, construction, and/or welding skills). A nutator (AKA nutating mixer or rotating mixer) is a gently rocking/rotating platform useful for continuously and gently mixing samples. They … Continue reading →

Posted in howto, methods, next generation sequencing | Leave a comment

Dr. Prepper

Posted on 5 Nov, 2011 by Brant Faircloth

Library preparation for next-gen sequencing has become a fact of life in many labs working with model and non-model organisms. The problems with library preparation are that (1) library prep is slow and (2) library prep is expensive. Generally speaking, … Continue reading →

Posted in methods, next generation sequencing | 5 Comments

Easing the pain of titration

Posted on 21 Sep, 2011 by Brant Faircloth

Quickly following up on Nick’s post re: Illumina Library Prep, Travis Glenn pointed me towards a manuscript in Nature Protocols that proposes an alternative to the oft-grumbled-about process of titrating libraries for 454/Ion Torrent sequencing: Zongli Zheng et al. Titration-free … Continue reading →

Posted in bioinformatics, howto, methods, next generation sequencing | 3 Comments

A Tweak to Illumina Library Prep

Posted on 19 Sep, 2011 by Nicholas Crawford

For those readers who are making Illumina libraries for NGS, which I assume is many of you, I’d like to direct you to this new paper by Sheila Fisher’s group at the Broad Institute. In this paper Fisher describes the … Continue reading →

Posted in bioinformatics, howto, methods, next generation sequencing | 1 Comment