https://RhettRautsaw.github.io/shiny/SequencingEstimator/
This Shiny application is designed to help you choose the right sequencing platform and estimate costs.
It is designed to estimate sequencing needs and costs for:
- Whole Genome Sequencing (WGS)
- Transcriptomics (RNA-seq)
- Whole Genome Bisulfite Sequencing (WGBS)
- Assay for Transposase Accessible Chromatin (ATAC-Seq)
- Double-digest Restriction-site Associated DNA Sequencing (ddRAD-Seq)
- However, given a desired coverage or number of reads (in millions), the different areas could be used for any type of sequencing.
Most of the information for sequencing platorms was obtained from Illumina. Illumina, PacBio, and Nanopore are constantly updating their platforms and I may not be able to keep up. Therefore, the option is provided to download an example database and update it yourself to re-upload.
The recommended number of reads and coverage for each type of sequencing are default input for all options (e.g. 20x for WGBS, 5 M reads for ddRAD-Seq).
There are many ways to download and run it.
It is hosted freely on my Digital Ocean Droplet: https://RhettRautsaw.github.io/shiny/SequencingEstimator/
This app can also be run through R:
library(shiny)
# Easiest way is to use runGitHub
runGitHub("SequencingEstimator", "RhettRautsaw")
# Run a tar or zip file directly
runUrl("https://github.com/RhettRautsaw/SequencingEstimator/archive/master.tar.gz")
runUrl("https://github.com/RhettRautsaw/SequencingEstimator/archive/master.zip")Or you can clone the git repository, then use runApp():
# First clone the repository with git. If you have cloned it into
# ~/SequencingEstimator, first go to that directory, then use runApp().
setwd("~/SequencingEstimator")
runApp()To run a Shiny app from a subdirectory in the repo or zip file, you can use the subdir argument. This repository happens to contain another copy of the app in inst/shinyapp/.
runGitHub("SequencingEstimator", "RhettRautsaw", subdir = "inst/shinyapp/")
runUrl("https://github.com/RhettRautsaw/SequencingEstimator/archive/master.tar.gz",
subdir = "inst/shinyapp/")