Splitting Hairs: poppr version 2.7

Positive Contact This version of poppr is a direct result of feedback that was prompted by my own feedback. I’m always grateful for eagle-eyed users of poppr who report when things are going awry. Recently, I had noticed that poppr was cited in a recent review on the analysis of polyploid genetic data (Meirmans, Liu, and Tienderen 2018) that highlighted some limitations with established methods, including Bruvo’s distance (Bruvo et al.

Installing the ABySS

A couple of weeks ago, I wanted to explore assembling 55 genomes of Sclerotinia sclerotiorum to check for structural rearrangements that could be caused by sub-lethal fungicide exposure. I figured the best way to do this was to assemble these genomes de novo as opposed to aligning them to a reference. This brought me to installing the ABySS de novo assembler on the HCC Tusker Cluster… and I can happily report, that after half a day of [command line bullshittery]1, I had ABySS up and running 👍.

Preprint Day!

Today, we finally published a preprint for a manuscript that spans over 15 years of data 🎉! Our massive Sclerotinia pop gen study out as preprint today @PeerJPreprints #AgriculturalScience #Genetics #Mycology — Dr. Sydney Everhart (@SydneyEverhart) October 3, 2017 Here’s the citation: Kamvar ZN, Amaradasa BS, Jhala R, McCoy S, Steadman JR, Everhart SE. (2017) Population structure and phenotypic variation of Sclerotinia sclerotiorum from dry bean in the United States.

Squishing a big bad bug

As I was preparing to push a new version of poppr to CRAN , this tweet (appropriately) came across my feed: Mistakes happen in science. What matters is what you do next. Anyone want to share a story of a mistake & how they handled it? — Adriana Porter Felt (@apf) September 10, 2017 The reason I was updating poppr was to fix a mistake I had made a few years ago.