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You might also take a look at this genomics-focused sqlite extension: https://github.com/mlin/GenomicSQLite As described in the repository README: This SQLite3 loadable extension adds features to the ubiquitous embedded RDBMS supporting applications in genome bioinformatics: genomic range indexing for overlap queries & joins in-SQL utility functions, e....


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The clodius tool puts tab-delimited data from a BED file into an rtree in a sqlite3 database: https://github.com/higlass/clodius/blob/c98bb16ade93402fcea3b749d705c52ea165b609/clodius/cli/aggregate.py#L457-L777 Data are stored in this database at multiple "zoom levels", which allows for fast queries at wide genomic extents: https://github.com/...


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