What problem does it solve?
It solves the problem of slow and error-prone handling of genomic interval files by providing efficient overlap detection, coverage generation, tokenization, and fragment/refget utilities in one toolkit.
Core Features & Use Cases
- Overlap Detection & IGD Indexing: Quickly find overlaps between BED region sets using an IGD-based index, supporting annotation and set operations; use it for regulatory element comparisons and variant-to-feature overlap queries.
- Coverage Track Generation (Uniwig): Convert BED/fragment intervals into coverage tracks such as WIG or BigWig for visualization and downstream analyses; use it for ATAC-seq/ChIP-seq coverage profiles.
- Genomic Tokenization for ML: Transform genomic regions into discrete tokens suitable for machine learning preprocessing, including integration patterns for genomic ML pipelines.
- Reference Sequence Management (refget): Load/reference FASTA-backed stores, extract subsequences, and compute/verify refget digests (GA4GH refget protocol).
- Fragment Processing & Scoring: Split fragments by barcodes/clusters and score enrichment against reference datasets for single-cell workflows.
Quick Start
Use the gtars skill to generate a BigWig coverage track from a fragments BED file and write it to coverage.bw.
