Introducing HybPiper

logo by Elliot Gardner

This week marks the “official” release of HybPiper, the bioinformatics pipeline I’ve been working on for most of my post-doc. We published a paper on the method, and demonstrated how it can be used for phylogenetics, in this month’s Applications in Plant Sciences (open access). This work was a collaboration between the Pleurocarpous…

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Transcriptome Tutorials

This summer we have an REU student from Amherst College who is sequencing Oenothera transcriptomes, and is learning both lab techniques and computational techniques. I’ve dusted off the bioinformatics tutorials I made for our Pleurocarp Tree of Life meeting, giving them some much-needed updates. I thought I would post them here…

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HybSeq Pipeline

Targeted bait capture (HybSeq) is a technique for sequencing many loci simultaneously based on bait sequences. Once the sequence data is generated, usually by Illumina, the next task is to sort the reads based on the target loci and assemble them. I generated this pipeline to work with data we…

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Structure Pipeline

Users of Structure (Pritchard et al, 2000) may be familiar with the interface of the BioHPC cluster at Cornell. Unfortunately, guest access was discontinued in May, 2011. If you have structure installed on your SGE supercomuting cluster, several features of the web-based BioHPC cluster interface can be replaced with a…

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