Category Archives: next generation sequencing

Q&A: Yannick Wurm wrangles RADseq to learn why some fire ants bow to more than one queen

Posted on 19 Feb, 2013 by Jeremy Yoder

Yannick Wurm grew up in Redwood City, California, and his initial plan was to design interfaces for Apple. But he went to university at the Institut National des Sciences Appliquées in Lyon—where, after two years of general engineering courses, the … Continue reading →

Posted in bioinformatics, interview, next generation sequencing | Tagged , , , | 1 Comment

Next-gen sequencing field guide, 2013 edition

Posted on 17 Jan, 2013 by Jeremy Yoder

Travis Glenn has updated his Field Guide to Next-Generation Sequencing, originally published in 2011, to account for changes to this almost axiomatically dynamic field. The 2013 update to the Field Guide tables is online here. Previous editions of the tables … Continue reading →

Posted in bioinformatics, data archiving, next generation sequencing | Tagged | Leave a comment

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

A comparison of bioinformatics programming languages

Posted on 20 Nov, 2012 by Mark Christie

The times are a-changin and most molecular ecologists and evolutionary biologists are no longer asking themselves, “Should I learn a programming language?”, but rather “Which programming language should I learn?”. There are a variety of programming languages that are used by … Continue reading →

Posted in bioinformatics, next generation sequencing, software | 10 Comments

One of these flycatchers is not like the other …

Posted on 31 Oct, 2012 by Jeremy Yoder

When you think about it, an awful lot of the things you can do with a genome sequence amount to lining it up next to another genome sequence, and then listing all the places where they differ. That’s more or … Continue reading →

Posted in next generation sequencing, speciation | Leave a comment

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

Linux: the glue that binds your next-generation sequencing analyses

Posted on 16 Oct, 2012 by Mark Christie

Would you like to use same operating system as 92% of the top 500 super computers?  Do you dig Japanese bullet trains, NASA, or the financial awesomeness that is the New York Stock Exchange?  Do you hate having to shell … Continue reading →

Posted in bioinformatics, next generation sequencing, population genetics | 5 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

2012 Update to the NGS Field Guide

Posted on 22 Apr, 2012 by Travis Glenn

After many months of essentially no updates worth mentioning, Ion Torrent announced their Proton sequencer on the morning of January 10th, followed later that same day by an announcement from Illumina of their upgraded HiSeq 2500. This of course, caused … Continue reading →

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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