Compressed-Resident Genomics: Full-Pipeline Device-Resident GPU LZ77 Decode with Position-Invariant Random Access (opens in new tab)

Genomic archives grow faster than decompression keeps up: the European Nucleotide Archive holds tens of petabytes of fastq.gz, and gzip is fundamentally sequential. GPU decompressors (nvCOMP DEFLATE at ~50GB/s on A100) decode whole files with no random access; CPU genomic tools (CRAM, samtools) support region seeks but only at CPU speed. We extend ACEAPEX, an absolute-offset parallel LZ77 codec included in the official lzbench 2.3 release, with ...