stephenturner/covcalc

Coverage / read count calculator for sequencing experiments

Coverage / Read Count Calculator

Shiny app to calculate how much sequencing you need to hit a target depth of coverage (or vice versa).

http://apps.bioconnector.virginia.edu/covcalc/

(Mirror: https://stephenturner.shinyapps.io/covcalc/)

covcalc's Issues

Insert Size

Nice looking app,

But I think you are missing an important parameter: insert size. If your insert size is greater than read length, then your app works just fine. But very often insert sizes are less than that, which means reads overlap, and you get less useful information.

As a result you would need more reads to meaningfully cover your genome, instead of covering a base twice from the same DNA fragment sequenced forward and reverse.

improvements

Good app. May I suggest improvements to account for real-life scenario. I would like to see this calculator take into account on-target coverage, instead of all coverage. We know that in NGS experiements many reads/bases fall in flanking introns. So the real coverage for a given output is lower that what is expected from the calculation above. So, taking insert-size into account will greatly help in getting the actual output needed for on-target coverage. Is it possible to perform this calculation based on the distribution of the inserts over a target region? Usually symmetrical, but the slope may vary? or one may use empirical data on on-target coverage as a ratio of on-target vs total? Additional improvements include accounting for duplicates, mapped-reads vs all reads. These may also be included as proportion of total reads, which the users can input based on empirical data from their labs (based on the sequencing instrument and chemistry etc etc)