Bradford Condon PhD

Bioinformatics, Web & Mobile Development


Software Carpentry

I am happy to announce I will be instructing a Software Carpentry Workshop at the University of Tennessee Knoxville. The workshop will be taught by myself, Meg Staton, and Drew Steen on December 18th and 19th, 2017 in 702 Strong Hall.

This workshop will cover the basics of:

  • Unix Shell
  • Git
  • R

Please visit the workshop website for more information and registration links.

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In a previous blog post, I announced my excitement for becoming a certified Software and Data Carpentry instructor. As I complete my checkout process, I also wanted to recap the most important points from the training. A lab meeting presentation of this recap cis available on google slides here.

Looking forward to teaching my first workshop in the next few months!

Data Carpentry Software Carpentry

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This week(September 25th & 26th 2017), I will be certified as a Software and Data Carpentry instructor. As of 2017-06-26, there were 968 instructors. Am I lucky number 1,000? Probably not. Still, exciting.

Data Carpentry Software Carpentry

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TreeSnap

Early this year, I joined Meg Staton’s group at the University of Tennessee as a mobile and web developer. My major project since then has been designing, coding, and releasing the mobile citizen science app TreeSnap. I think it’s a fantastic project, and I’d love it if you visited the app’s website to learn more.

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This post is part 10 of a series on bioinformatics file formats, written for the 2017 UK-KBRIN Essentials of Next Generation Sequencing Workshop at the University of Kentucky.

Discovar

DISCOVAR is a new genome assembler and variant caller developed by the broad institute. As of this writing,it takes as input Illumina reads of length 250 or longer produced on MiSeq or HiSeq 2500. To learn more, read the entire DISCOVAR manual here.

The assembly output

The final output assembly will take the form of OUT_HEAD.final.*, where OUT_HEAD is set by the user. Below let’s assume we’ve set OUT_HEAD to out.

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This post is part 8 of a series on bioinformatics file formats, written for the 2017 UK-KBRIN Essentials of Next Generation Sequencing Workshop at the University of Kentucky.

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This post is part 8 of a series on bioinformatics file formats, written for the 2017 UK-KBRIN Essentials of Next Generation Sequencing Workshop at the University of Kentucky.

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This post is part 7 of a series on file formats, written for the 2017 UK-KBRIN Essentials of Next Generation Sequencing Workshop at the University of Kentucky.

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This post is part 6 of a series on file formats, written for the 2017 UK-KBRIN Essentials of Next Generation Sequencing Workshop at the University of Kentucky.

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This post is part 5 of a series on file formats, written for the 2017 UK-KBRIN Essentials of Next Generation Sequencing Workshop at the University of Kentucky.

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