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 https://t.co/O85hUURi2s #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.

20,000 downloads under the C(RAN)

My R package poppr hit over 20,000 downloads on CRAN. I thought this would be a nice opportunity to briefly talk about what initiated the development. Before that, let’s look at the cumulative number of downloads: CRAN you dig it? Thanks to the fantastic cranlogs package, assessing the download history of a package is quite simple (with the caveat that these are logs from the rstudio mirror, so the value is almost always lower than the true value).

Recreating Figure 3

Motivation In February of 2016, I got an email asking if I could provide the code to recreate figure three from my article in Phytopathology on the outbreak of Phytophthora ramorum in Curry County OR from 2001 to 2014 (paywalled, but you can find a copy here). While I have the code used for the analysis on github, it’s a lot of stuff to sort through, considering that it was my first foray in attempting a reproducible analysis, so for this post, I’m going to recreate it using current tools.