Sus scrofa

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mSusScr4 172.90 Gbp N/A 80.9 GiB
PacBio HiFi (.bam) mSusScr4 179.37 Gbp N/A 593.2 GiB
Arima mSusScr4 174.46 Gbp N/A 93.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 8 June 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mSusScr4 PacBio HiFi (.fq) 172.90 Gbp N/A 80.9 GiB
PacBio HiFi (.bam) 179.37 Gbp N/A 593.2 GiB
Arima 174.46 Gbp N/A 93.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 8 June 2026.
Assemblies
Individual 4 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 22 June 2026
mSusScr4.HiC.hap1.20260622.fasta.gz (672.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 192.42 Mbp 1 286.21 Mbp
20 3 158.73 Mbp 3 173.88 Mbp
30 5 121.21 Mbp 4 161.39 Mbp
40 8 103.95 Mbp 6 146.00 Mbp
50 10 93.48 Mbp 8 142.56 Mbp
60 13 78.24 Mbp 9 141.51 Mbp
70 18 49.14 Mbp 11 136.27 Mbp
80 24 41.04 Mbp 13 110.87 Mbp
90 31 31.94 Mbp 16 80.66 Mbp
100 258 9.46 Kbp 212 9.46 Kbp
1.000x 258 2.60 Gbp 212 2.60 Gbp
NG based on genome size .
Individual 4 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 22 June 2026
mSusScr4.HiC.hap2.20260622.fasta.gz (639.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 191.59 Mbp 1 290.32 Mbp
20 3 157.37 Mbp 2 224.73 Mbp
30 5 119.01 Mbp 4 160.37 Mbp
40 7 105.71 Mbp 6 146.68 Mbp
50 10 98.73 Mbp 7 143.73 Mbp
60 12 86.90 Mbp 9 141.65 Mbp
70 16 64.06 Mbp 11 135.00 Mbp
80 21 42.72 Mbp 13 92.47 Mbp
90 28 24.83 Mbp 16 69.57 Mbp
100 178 24.80 Kbp 146 24.80 Kbp
1.000x 178 2.54 Gbp 146 2.54 Gbp
NG based on genome size .
Individual 4 Mitochondrial Assembly
Version assembly_MT_rockefeller from 22 June 2026
mSusScr4.MT.20260622.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mSusScr4.yml (view)
species: Sus scrofa
specimen: mSusScr4
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Sus_scrofa/mSusScr4/assembly_vgp_HiC_2.0/mSusScr4.HiC.hap1.20260622.fasta.gz
hap2: s3://genomeark/species/Sus_scrofa/mSusScr4/assembly_vgp_HiC_2.0/mSusScr4.HiC.hap2.20260622.fasta.gz
pretext_hap1: s3://genomeark/species/Sus_scrofa/mSusScr4/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mSusScr4_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Sus_scrofa/mSusScr4/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mSusScr4_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Sus_scrofa/mSusScr4/assembly_vgp_HiC_2.0/evaluation/merqury/mSusScr4_png/
pacbio_read_dir: s3://genomeark/species/Sus_scrofa/mSusScr4/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Sus_scrofa/mSusScr4/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy3)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.9)
  - VGP4 HiFi HiC assembly workflow (v0.6)
  - VGP8 HiC scaffolding workflow (v3.5) with mapq=10
  - VGP9 decontamination workflow (v1.3)
  - Pre-curation workflow (20250526 update) with mapq=10, keep HiC duplicates and generate standard resolution map
notes: This was a Hifiasm-HiC assembly of mSusScr4 resulting in two haplotype assemblies. HiC data were generated using the Arima library prep kit, and require trimming the first 5 bp off from the 5' end of both read files. The restriction enzymes used were the Arima v2 kit, so the cutting sites are GATC, GANTC, CTNAG, TTAA. The QC step compleasm was run locally (v0.2.6). 
Data Use Policy

Samples and data come from a variety of sources. To support fair and productive use of this data, please abide by the Data Use Policy and contact Erich D. Jarvis, ejarvis@rockefeller.edu, with any questions.