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Ragnar {Groot Koerkamp}
@curiouscoding.nl

I've been working on Pandedup the past weeks: a tool to quickly dedup the k-mer content of a pangenome (read: HPRCv2). Just uploaded a k=64 SPSS (k-mer spectrum preserving string set) as well: zenodo.org/records/2172... This reduces the ~1.5Tbp input to just 10.6Gbp. github.com/RagnarGrootK...

github.comGitHub - RagnarGrootKoerkamp/pandedup: Pandedup uses minimizers to build a quick & dirty k-mer spectrum (SPSS) from a .AGC pangenome.Pandedup uses minimizers to build a quick & dirty k-mer spectrum (SPSS) from a .AGC pangenome. - RagnarGrootKoerkamp/pandedup
Ragnar {Groot Koerkamp}
@curiouscoding.nl

Applications include: searching off-target matches of crispr guides across all of HPRCv2 using Sassy (in particular using the work-in-progress GPU version), and a smaller/more accurate baseline for host-decontamination using Deacon.

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