excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies

Area of Science:

• Genomics and Bioinformatics
• Computational Biology
• Data Science

Background:

• Exclusion regions in reference genomes, characterized by abnormal short sequencing read pileups, can obscure biological signals.
• Existing exclusion region sets are fragmented across various sources (e.g., ENCODE, GitHub), causing uncertainty in selection.
• Gap regions like centromeres and telomeres present unique challenges for generating accurate exclusion sets.

Purpose of the Study:

• To systematically assemble, annotate, and provide unified access to diverse genomic exclusion region sets.
• To generate new exclusion sets for the latest human T2T-CHM13 and mouse GRCm39 genome assemblies.
• To offer guidance on selecting the most appropriate exclusion sets for specific genomic analyses.

Main Methods:

• Development of the excluderanges R/Bioconductor data package.
• Systematic curation and annotation of existing and newly generated exclusion region sets.
• Integration of data access via the BEDbase.org API.

Main Results:

• The excluderanges package provides unified access to 82 GenomicRanges objects.
• These objects cover six organisms, multiple genome assemblies, and various types of exclusion regions.
• Recommendations are provided: hg38.Kundaje.GRCh38_unified_blacklist for human hg38, and Blacklist tool-generated sets for other organisms.

Conclusions:

• The excluderanges package simplifies the process of identifying and utilizing genomic exclusion regions.
• This resource enhances the reliability of biological signal detection, particularly in differential analysis.
• Standardized access to curated exclusion sets facilitates reproducible genomic research.