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Hi, if you found this page you are probably looking for some additional information on WISECONDOR.

Publication

The algorithm used is described in the paper which can be found here:
WISECONDOR: detection of fetal aberrations from shallow sequencing maternal plasma based on a within-sample comparison scheme

Master version (new)

When updating to the new version, follow the README.md file in the repository.
To understand the output, read Plots to understand the new type of plotting provided.
While the README.md does contain a changelist, the method changes are better described on the Methods page.
Additionally, if you want to look into WISECONDOR closely, improve or customize the scripts, you may enjoy this detailed explanation of the files WISECONDOR now creates: File format.

Legacy version information

Everything below is written for the legacy version, the new version has significant differences in implementation, inputs, outputs, and results in general. While lots of the answers are not changed that much (theories didn't change that much), consider everything here backup information if something is not answered using the pages linked above.

Quick guide

If you are not very tech-savvy, I created an automated script to solve most complications: WISECONDOR on autopilot: run.sh. Be aware of its limitations: although it usually runs without issues, you have no control over the options and arguments available to tweak WISECONDOR to your likings.

Detailed information

Does WISECONDOR ... ?
Getting WISECONDOR to work
Understanding the input
Understanding the output
View results

To help people getting started, I created an Example Pipeline

Additional downloads

I received word that an Ion Torrent plugin for WISECONDOR is now available. I have no such device myself so I cannot provide support but you can find the project here:
Ion-WISECONDOR