Covcalc: Shiny App for Calculating Coverage Depth or Read Counts for Sequencing Experiments

June 1, 2016
By

(This article was first published on Getting Genetics Done, and kindly contributed to R-bloggers)

How many reads do I need? What’s my sequencing depth? These are common questions I get all the time. Calculating how much sequence data you need to hit a target depth of coverage, or the inverse, what’s the coverage depth given a set amount of sequencing, are both easy to answer with some basic algebra. Given one or the other, plus the genome size and read length/configuration, you can calculate either. This was inspired by a similar calculator written by James Hadfield, and was an opportunity for me to create my first Shiny app.

Check out the app here:
http://apps.bioconnector.virginia.edu/covcalc/

And the source code on GitHub:
https://github.com/stephenturner/covcalc

Give it your read length, whether you’re using single- or paired-end sequencing, select a genome or enter your own. Then, select whether you want to calculate (a) the number of reads you need to hit a target depth of coverage, or (b) the coverage depth you’ll hit given a set number of sequencing reads. Once you make the selection, use the slider to adjust either the desired coverage or number of reads sequenced, and the output text below is automatically updated.

Shiny App: Coverage / Read Count Calculator

To leave a comment for the author, please follow the link and comment on their blog: Getting Genetics Done.

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