ToTem: a tool for variant calling pipeline optimization.

ABSTRACT:

Background

High-throughput bioinformatics analyses of next generation sequencing (NGS) data often require challenging pipeline optimization. The key problem is choosing appropriate tools and selecting the best parameters for optimal precision and recall.

Results

Here we introduce ToTem, a tool for automated pipeline optimization. ToTem is a stand-alone web application with a comprehensive graphical user interface (GUI). ToTem is written in Java and PHP with an underlying connection to a MySQL database. Its primary role is to automatically generate, execute and benchmark different variant calling pipeline settings. Our tool allows an analysis to be started from any level of the process and with the possibility of plugging almost any tool or code. To prevent an over-fitting of

SUBMITTER: Tom N 

PROVIDER: S-EPMC6020218 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature