HPRCv2 k-mer spectrum (SPSS)

This is a k=64 k-mer spectrum (or SPSS, spectrum preserving string set) of HPRCv2. The input is the 3.3 GB AGC file at this url, containing a total of 466 human genomes. The output is a 3.0 GB compressed fasta file with many small contigs that contains all k-mers of HPRCv2. The output is not minimal: some k-mers are duplicated, and a smaller representation could be possible by stitching together unitigs. No deduplication is done across k-mers and their reverse-complement. This file was built using pandedup with parameters k=64, w=10 (and defaults k'=8, anti-lexicographic minimizers) in 10 minutes on a 64-core machine, using ~100GB of RAM.

Keywords

k-mer spectrum, SPSS, HPRCv2

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