triform

Triform is a software tool that identifies transcription factor binding sites in Chromatin immunoprecipitation combined with high-throughput sequencing (ChIP-Seq) profiles. This frequently used method allows researchers to identify active binding sites that manifest as peaks in enrichment profiles when the sequencing reads are mapped to a reference genome. However, the profiles are often noisy, which makes it difficult to reliably identify all significantly enriched regions with an acceptable false discovery rate.

To overcome this challenge, the Triform algorithm was developed. It uses model-free statistics to identify peak-like distributions of sequencing reads while taking advantage of improved peak definition in combination with known characteristics of ChIP-Seq data. Triform outperforms several of them in identifying representative peak profiles in curated benchmark datasets compared to other existing methods. Furthermore, Triform can also identify peaks more consistent with biological function, which is a crucial aspect in studying transcription factors.

Triform can generate novel information on transcription factor binding in repeat regions, a challenge in many ChIP-Seq experiments.