Orycteropus afer

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mOryAfe1 221.16 Gbp N/A 104.1 GiB
PacBio HiFi (.bam) mOryAfe1 225.44 Gbp N/A 735.7 GiB
Arima mOryAfe1 398.80 Gbp N/A 217.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 16 June 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mOryAfe1 PacBio HiFi (.fq) 221.16 Gbp N/A 104.1 GiB
PacBio HiFi (.bam) 225.44 Gbp N/A 735.7 GiB
Arima 398.80 Gbp N/A 217.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 16 June 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 28 July 2025
mOryAfe1.HiC.hap1.20250728.fasta.gz (1.2 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 488.55 Mbp 1 1.76 Gbp
20 3 291.67 Mbp 1 1.76 Gbp
30 4 271.60 Mbp 1 1.76 Gbp
40 6 237.96 Mbp 2 0.65 Gbp
50 8 185.58 Mbp 2 0.65 Gbp
60 12 124.31 Mbp 3 0.51 Gbp
70 16 97.36 Mbp 4 480.44 Mbp
80 22 63.60 Mbp 5 429.96 Mbp
90 33 22.37 Mbp 7 156.57 Mbp
100 512 6.69 Kbp 456 6.69 Kbp
1.000x 512 4.69 Gbp 456 4.69 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 28 July 2025
mOryAfe1.HiC.hap2.20250728.fasta.gz (1.1 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 0.56 Gbp 1 1.71 Gbp
20 2 327.53 Mbp 1 1.71 Gbp
30 4 235.38 Mbp 1 1.71 Gbp
40 6 215.94 Mbp 2 1.50 Gbp
50 8 179.99 Mbp 2 1.50 Gbp
60 11 141.03 Mbp 2 1.50 Gbp
70 14 122.27 Mbp 2 1.50 Gbp
80 18 89.42 Mbp 3 471.32 Mbp
90 25 36.09 Mbp 4 429.90 Mbp
100 384 19.13 Kbp 319 19.13 Kbp
1.000x 384 4.32 Gbp 319 4.32 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 28 July 2025
mOryAfe1.MT.20250728.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mOryAfe1.yml (view)
species: Orycteropus afer
specimem: mOryAfe1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Orycteropus_afer/mOryAfe1/assembly_vgp_HiC_2.0/mOryAfe1.HiC.hap1.20250728.fasta.gz
hap2: s3://genomeark/species/Orycteropus_afer/mOryAfe1/assembly_vgp_HiC_2.0/mOryAfe1.HiC.hap2.20250728.fasta.gz
pretext_hap1: s3://genomeark/species/Orycteropus_afer/mOryAfe1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mOryAfe1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Orycteropus_afer/mOryAfe1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mOryAfe1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Orycteropus_afer/mOryAfe1/assembly_vgp_HiC_2.0/evaluation/merqury/mOryAfe1_png/
pacbio_read_dir: s3://genomeark/species/Orycteropus_afer/mOryAfe1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Orycteropus_afer/mOryAfe1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.1)
  - VGP1 genomic profiling workflow (v0.3)
  - VGP4 HiFi HiC assembly workflow (v0.3.8)
  - VGP8 HiC scaffolding workflow (v2.0)
  - VGP9 decontamination workflow kraken2 with database PlusPF 2022 (workflow included a step to remove scaffold >1 billion base pair to avoid blast crushing)
  - Pre-curation worklfow (v1.0beta6)
notes: This was a Hifiasm-HiC assembly of mOryAfe1 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.