Representations of k-mer sets of genomic datasets of different kinds

This record contains selected exact epresentations of k-mer sets, for k = 15, 31, 63 (and 127 where feasible) of selected genomic datasets of different kinds. Filename format: <dataset>.S_<representation>.k_<k>.z_<min_freq>.fa.xz, where min_freq is the threshold for filtering k-mers (1=all k-mers of source dataset, 2=k-mers that occur at least twice in the source data). The source genomic datasets are: E. coli pan-genome, obtained as the union of the E. coli genomes from the 661k collection with high-quality filtering applied (HQ). Metagenomic sample SRS063932 (Illumina raw reads) of human microbiome with accession SRX023459, download from https://www.hmpdacc.org/hmp/HMASM/. The fastq files were converted to FASTA files using seqtk seq -A -C. Human RNA-seq Illumina raw reads with accession SRX348811, downloaded using the prefetch tool from the SRA toolkit and then converted into the FASTA format by fastq-dump --split-3 --fasta. Human genome Illumina raw reads with accession SRX016231, downloaded using the prefetch tool from the SRA toolkit and then converted into the FASTA format by fastq-dump --split-3 --fasta. Human genome assembly chm13v2.0 (T2T), downloaded from https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0.fa.gz. Human pangenome was obtained from human472.agc from https://zenodo.org/records/14854401 (version 3.0), with individual genome assemblies extracted using AGC (v3.2.1) with agc getcol -g 9 -l 2000000000 -v 2 -o out_dir human472.agc The computed k-mer set representations are: unitigs: computed using GGCAT v2.2.0 simpligs (maximal simplitigs, not necessarily optimal): computed from unitigs using GGCAT v2.2.0, with --simplitigs greedy matchtigs: computed from unitigs using GGCAT v2.2.0, with --greedy-matchtigs masked superstrings, greedily computed from either simplitigs, or unitigs (if simplitigs were not available) using the Bigreedy algorithm implemented in Kmercamel v2.3.1. In several cases, it was not possible to compute greedy matchtigs or even simplitigs within 24 h and 200 GB RAM limits.