Category Archives: bioinformatics

Using GitHub with R and RStudio

A few weeks back, the Molecular Ecologist released an article about GitHub and also created an organization where you can fork or simply download code shared by the Molecular Ecology community. A few of you out there may still be … Continue reading

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Posted in bioinformatics, howto, R, software | 7 Comments

Sequencer to the stars

No single person is responsible for the revolution in genetic data collection that has reshaped biology over just a handful of decades, but if you had to make a list of people deserving credit, Craig Venter’s name would be among … Continue reading

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Posted in bioinformatics, book review, genomics | Leave a comment

Want to share your code?

In this line of work, we have all encountered tasks that are tedious, time consuming, and repetitive.  (Or if not, maybe give it a bit more time.) When confronted with these situations, people tend to fall into one of two … Continue reading

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Posted in bioinformatics, community, genomics, howto, methods, next generation sequencing, phylogenetics, population genetics, quantitative genetics, R, software, theory | 13 Comments

How to Backup and Store your Next-Generation Sequencing (NGS) data

Congratulations!  You have recently received a file path to retrieve your hard-earned next-generation sequencing data.  You quickly transfer the files to the computing cluster you work on or perhaps, if you only have a few lanes of data, to your … Continue reading

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Posted in bioinformatics, data archiving, genomics, howto | 1 Comment

Q&A: Julian Catchen helps us dig into STACKS – Part II

As promised, below is part II of our interview with Julian Catchen. These questions focus more on the specifics of using stacks (i.e., user-related questions). Please see the first post if you are interested a general overview. Even more information, … Continue reading

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Q&A: Julian Catchen helps us dig into STACKS

Julian Catchen is a post-doctoral researcher at the University of Oregon, where he uses computational solutions to facilitate the analysis of next-generation sequencing data. Prior to obtaining his PhD, Julian worked for both Intel and IBM, experiences that no doubt … Continue reading

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Posted in bioinformatics, genomics, howto, interview, methods | 2 Comments

Phylogeny-aware comparisons of microbial communities – EdgePCA and Squash Clustering

I’m jumping on the bandwagon with a blog post about this new PLoS ONE paper (taking the lead from the man in charge in my lab) because the algorithms are just so exciting: Matsen FA IV, Evans SN. (2013) Edge Principal … Continue reading

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Posted in bioinformatics, genomics, next generation sequencing, software | Tagged , , , , , , , | 1 Comment

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

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

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Next-gen sequencing field guide, 2013 edition

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

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A comparison of bioinformatics programming languages

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

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