Belonogaster genome reports

# Belonogaster juncea genome reports, Hi-C contact map and satellite DNA, version 2 This version keeps the two Dovetail/Cantata Bio reports from version 1:- `IOW_rep_wtdbg.html`: assembly and BlobTools contamination report;- `IOW2052_rep_hirise.html`: HiRise Hi-C scaffolding report. It adds the files behind Figure 1b and the satellite DNA results of the *B. juncea* genome paper (Wyatt et al.). Code: https://github.com/Sumner-lab/Belonogaster_genome_paper/tree/main/HiC_and_satellite ## Omni-C contact map and assembly layout (Figure 1b) The Omni-C reads themselves are in NCBI SRA as SRR41179205 (BioProject PRJNA1357342). | File | Contents ||---|---|| `B_junceaGenome.0.hic` | Juicer/3D-DNA (version 180114) contact map of the Omni-C reads. It is drawn in the original 3D-DNA layout. || `B_junceaGenome.0.assembly` | the original 3D-DNA layout || `B_junceaGenome.0.review.assembly` | the layout after manual curation in Juicebox, i.e. the final assembly || `review_layout_to_final_scaffolds.tsv` | how the curated scaffolds match the final `HiC_scaffold_N` names (GCA_057814355.1) || `contacts_chr1-39_250kb.npz` | contact counts in 250-kb bins for HiC_scaffold_1–39, in final-assembly order. This is the matrix plotted in Figure 1b (NumPy; arrays `N`, `res`, `names`, `starts`, `ends`). | ## Tandem repeats and the 296-bp satellite | File | Contents ||---|---|| `B_juncea_trf.txt.gz` | Tandem Repeats Finder v4.09.1 output for the final assembly (parameters 2 7 7 80 10 50 2000, `-ngs`, maximum array length 10 Mb) || `trf_summary.tsv` | tandem-repeat and satellite totals for HiC_scaffold_1–39. Satellite: 63.7 Mb, 20.5%. || `satellite_296bp_consensus.fa` | consensus monomer of the 296-bp satellite |