Segtools

Segtools is a software toolkit that simplifies and automates the exploration of genomic segmentations. As genome-wide experiments and annotations become more prevalent, researchers increasingly require tools to help interpret data at this scale. Many functional genomics experiments involve partitioning the genome into labeled segments, such that segments sharing the same label exhibit one or more biochemical or functional traits. For example, a collection of ChlP-seq experiments yields a compendium of peaks, each labeled with one or more associated DNA-binding proteins. Similarly, manually or automatically generated annotations of functional genomic elements, including cis-regulatory modules and protein-coding or RNA genes, can also be summarized as genomic segmentations.

Segtools offers interacting tools that can be pipelined and summarized in a single HTML page. It operates with various tools, each providing one summarization mode. This process makes exploring genomic segmentations more convenient and powerful for researchers.

Segtools have been demonstrated using human histone modification data sets and Plasmodium falciparum local chromatin structure data sets. The software provides one mode of summarization. However, the various tools can be pipelined, providing different modes of summarization. These tools can be summarized in a single HTML page, making it easier for researchers to view the results.