Dicerorhinus sumatrensis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mDicSum1 109.05 Gbp N/A 50.4 GiB
PacBio HiFi (.bam) mDicSum1 107.80 Gbp N/A 353.6 GiB
Arima mDicSum1 234.40 Gbp N/A 121.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 23 April 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mDicSum1 PacBio HiFi (.fq) 109.05 Gbp N/A 50.4 GiB
PacBio HiFi (.bam) 107.80 Gbp N/A 353.6 GiB
Arima 234.40 Gbp N/A 121.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 23 April 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 12 September 2025
mDicSum1.HiC.hap1.20250912.fasta.gz (728.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 53.43 Mbp 3 99.66 Mbp
20 10 44.22 Mbp 6 93.81 Mbp
30 17 33.53 Mbp 9 86.34 Mbp
40 25 30.73 Mbp 12 77.43 Mbp
50 35 23.51 Mbp 16 66.35 Mbp
60 47 20.04 Mbp 20 63.83 Mbp
70 66 12.32 Mbp 25 51.22 Mbp
80 91 8.90 Mbp 30 44.25 Mbp
90 136 4.01 Mbp 37 34.01 Mbp
100 640 12.48 Kbp 430 12.48 Kbp
1.000x 640 2.70 Gbp 430 2.70 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 12 September 2025
mDicSum1.HiC.hap2.20250912.fasta.gz (692.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 70.91 Mbp 3 100.45 Mbp
20 8 44.63 Mbp 6 94.14 Mbp
30 15 36.02 Mbp 8 88.68 Mbp
40 22 32.13 Mbp 12 75.32 Mbp
50 31 27.64 Mbp 15 66.40 Mbp
60 43 18.49 Mbp 20 57.93 Mbp
70 59 12.82 Mbp 24 51.78 Mbp
80 86 7.06 Mbp 30 39.38 Mbp
90 145 2.37 Mbp 37 30.92 Mbp
100 1114 15.63 Kbp 910 15.63 Kbp
1.000x 1114 2.61 Gbp 910 2.61 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 11 September 2025
mDicSum1.MT.20250911.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mDicSum1.yml (view)
species: Dicerorhinus sumatrensis
specimem: mDicSum1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Dicerorhinus_sumatrensis/mDicSum1/assembly_vgp_HiC_2.0/mDicSum1.HiC.hap1.20250912.fasta.gz
hap2: s3://genomeark/species/Dicerorhinus_sumatrensis/mDicSum1/assembly_vgp_HiC_2.0/mDicSum1.HiC.hap2.20250912.fasta.gz
pretext_hap1: s3://genomeark/species/Dicerorhinus_sumatrensis/mDicSum1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mDicSum1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Dicerorhinus_sumatrensis/mDicSum1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mDicSum1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Dicerorhinus_sumatrensis/mDicSum1/assembly_vgp_HiC_2.0/evaluation/merqury/mDicSum1_png/
pacbio_read_dir: s3://genomeark/species/Dicerorhinus_sumatrensis/mDicSum1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Dicerorhinus_sumatrensis/mDicSum1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.11)
  - VGP8 HiC scaffolding workflow (v2.2) mapq set to 10
  - VGP9 decontamination workflow (v0.7) with database PlusPF 2022
  - Pre-curation worklfow (v1.0beta6) mapq set to 10
notes: This was a Hifiasm-HiC assembly of mDicSum1 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.
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.