Hecate: A Modular Genomic Compressor
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arXiv
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| Format: | Preprint |
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2026
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| author | Szewczyk, Kamila Rahmann, Sven |
| author_facet | Szewczyk, Kamila Rahmann, Sven |
| contents | We present Hecate, a modular lossless genomic compression framework. It is designed around uncommon but practical source-coding choices. Unlike many single-method compressors, Hecate treats compression as a conditional coding problem over coupled FASTA/FASTQ streams (control, headers, nucleotides, case, quality, extras). It uses per-stream codecs under a shared indexed block container. Codecs include alphabet-aware packing with an explicit side channel for out-of-alphabet residues, an auxiliary-index Burrows-Wheeler pipeline with custom arithmetic coding, and a blockwise Markov mixture coder with explicit model-competition signaling. This architecture yields high throughput, exact random-access slicing, and referential mode through streamwise binary differencing. In a comprehensive benchmark suite, Hecate provides the best compression vs. speed trade-offs against state-of-the-art established tools (MFCompress, NAF, bzip3, AGC), with notably stronger behaviour on large genomes and high-similarity referential settings. For the same compression ratio, Hecate is 2 to 10 times faster. When given the same time budget as other algorithms, Hecate achieves up to 5% to 10% better compression. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2603_15390 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | Hecate: A Modular Genomic Compressor Szewczyk, Kamila Rahmann, Sven Data Structures and Algorithms Genomics We present Hecate, a modular lossless genomic compression framework. It is designed around uncommon but practical source-coding choices. Unlike many single-method compressors, Hecate treats compression as a conditional coding problem over coupled FASTA/FASTQ streams (control, headers, nucleotides, case, quality, extras). It uses per-stream codecs under a shared indexed block container. Codecs include alphabet-aware packing with an explicit side channel for out-of-alphabet residues, an auxiliary-index Burrows-Wheeler pipeline with custom arithmetic coding, and a blockwise Markov mixture coder with explicit model-competition signaling. This architecture yields high throughput, exact random-access slicing, and referential mode through streamwise binary differencing. In a comprehensive benchmark suite, Hecate provides the best compression vs. speed trade-offs against state-of-the-art established tools (MFCompress, NAF, bzip3, AGC), with notably stronger behaviour on large genomes and high-similarity referential settings. For the same compression ratio, Hecate is 2 to 10 times faster. When given the same time budget as other algorithms, Hecate achieves up to 5% to 10% better compression. |
| title | Hecate: A Modular Genomic Compressor |
| topic | Data Structures and Algorithms Genomics |
| url | https://arxiv.org/abs/2603.15390 |