Bradford Condon PhD

Bioinformatics, Web & Mobile Development


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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This post is part 4 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 3 of a series on file formats, written for the 2017 UK-KBRIN Essentials of Next Generation Sequencing Workshop at the University of Kentucky. The conference website is hosted here.

General transfer format (GTF), also known as General Feature Format (GFF) 2.0, is the format for transcripts in exercise 4, RNAseq. For more details, please see the ensembl guide to GFF.

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Expanding your horizons header NSF epscor

On April 29th 2017, the Expanding Your Horizons conference came to Kentucky for the first time. The conference was funded by an NSF EPSCoR (National Science Foundation Experimental Program to Stimulate Competitive Research for Education and Outreach) grant which I, along with Ellen Crocker and Susan Odom, was a PI on. I’m very grateful for all of the volunteers, corporate partners, parents, teachers, and students who made this conference a success.

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