d4explorer documentation

Screenshot of d4explorer coverage page

About

d4explorer is a simple interactive application to plot coverage data in d4 format. The main purpose is to provide a tool for selecting coverage thresholds that define accessible sites in a non-model organism resequencing project for which it may be difficult to generate all sites VCF output.

Quickstart

Install d4explorer from github:

python -m pip install "d4explorer @ git+https://github.com/percyfal/d4explorer"

Then you need to run the preprocesscommand to process one or multiple d4 files.

d4explorer preprocess file1.d4 file2.d4 ...

This will run d4 hist behind the scenes to generate a d4 histogram file which subsequently will be stored in the d4explorer cache (by default directory cache).

Adding an annotation file to the preprocessing step will furthermore stratify results along regions:

d4explorer preprocess --annotation-file annotation.gff file1.d4 file2.d4 ...

Once the cache is populated, you can serve the app:

d4explorer serve

This will launch the d4explorer app at http://localhost:5006. The web page will display a list of datasets, and once loaded, the histograms are sampled to produce coverage plots over features. By modifying the coverage range and monitoring the feature size indicators you can decide on appropriate thresholds for your data.