LOGIQA: a database dedicated to long-range genome interactions quality assessment

BMC Genomics. 2016 May 16;17:355. doi: 10.1186/s12864-016-2642-1.

Abstract

Background: Proximity ligation-mediated methods are essential to study the impact of three-dimensional chromatin organization on gene programming. Albeit significant progress has been made in the development of computational tools that assess long-range chromatin interactions, next to nothing is known about the quality of the generated datasets.

Method: We have developed LOGIQA ( www.ngs-qc.org/logiqa ), a database hosting quality scores for long-range genome interaction assays, accessible through a user-friendly web-based environment.

Results: Currently, LOGIQA harbors QC scores for >900 datasets, which provides a global view of their relative quality and reveals the impact of genome size, coverage and other technical aspects. LOGIQA provides a user-friendly dataset query panel and a genome viewer to assess local genome-interaction maps at different resolution and quality-assessment conditions.

Conclusions: LOGIQA is the first database hosting quality scores dedicated to long-range chromatin interaction assays, which in addition provides a platform for visualizing genome interactions made available by the scientific community.

Keywords: Chromatin architecture; HiC; Quality.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods
  • Databases, Genetic*
  • Epistasis, Genetic
  • Genetic Heterogeneity
  • Genome*
  • Genomics / methods*
  • Reproducibility of Results
  • Software*
  • Web Browser