Capra nubiana

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mCapNub1 127.56 Gbp N/A 59.2 GiB
PacBio HiFi (.bam) mCapNub1 128.94 Gbp N/A 417.3 GiB
Arima mCapNub1 215.40 Gbp N/A 117.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 18 April 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mCapNub1 PacBio HiFi (.fq) 127.56 Gbp N/A 59.2 GiB
PacBio HiFi (.bam) 128.94 Gbp N/A 417.3 GiB
Arima 215.40 Gbp N/A 117.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 18 April 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 21 May 2025
mCapNub1.HiC.hap1.20250521.fasta.gz (728.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 137.52 Mbp 2 137.52 Mbp
20 5 119.94 Mbp 4 125.35 Mbp
30 7 112.92 Mbp 7 118.81 Mbp
40 9 106.72 Mbp 9 108.93 Mbp
50 12 91.49 Mbp 12 95.38 Mbp
60 15 82.64 Mbp 15 83.49 Mbp
70 19 73.02 Mbp 18 73.16 Mbp
80 23 62.47 Mbp 22 62.61 Mbp
90 28 45.35 Mbp 27 51.63 Mbp
100 370 19.70 Kbp 290 19.70 Kbp
1.000x 370 2.77 Gbp 290 2.77 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 21 May 2025
mCapNub1.HiC.hap2.20250521.fasta.gz (704.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 137.53 Mbp 2 168.27 Mbp
20 5 120.19 Mbp 3 158.61 Mbp
30 7 112.11 Mbp 6 119.11 Mbp
40 9 108.65 Mbp 8 108.65 Mbp
50 12 94.84 Mbp 11 94.84 Mbp
60 15 82.73 Mbp 14 82.73 Mbp
70 19 67.30 Mbp 17 72.73 Mbp
80 24 51.78 Mbp 22 60.70 Mbp
90 30 23.25 Mbp 27 45.89 Mbp
100 631 18.12 Kbp 558 18.12 Kbp
1.000x 631 2.76 Gbp 558 2.76 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 16 May 2025
mCapNub1.MT.20250516.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mCapNub1.yml (view)
species: Capra nubiana
specimem: mCapNub1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Capra_nubiana/mCapNub1/assembly_vgp_HiC_2.0/mCapNub1.HiC.hap1.20250521.fasta.gz
hap2: s3://genomeark/species/Capra_nubiana/mCapNub1/assembly_vgp_HiC_2.0/mCapNub1.HiC.hap2.20250521.fasta.gz
pretext_hap1: s3://genomeark/species/Capra_nubiana/mCapNub1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mCapNub1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Capra_nubiana/mCapNub1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mCapNub1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Capra_nubiana/mCapNub1/assembly_vgp_HiC_2.0/evaluation/merqury/mCapNub1_png/
pacbio_read_dir: s3://genomeark/species/Capra_nubiana/mCapNub1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Capra_nubiana/mCapNub1/genomic_data/arima/
pipeline:
  - hifiasm (0.24.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
notes: This was a Hifiasm-HiC assembly of mCapNub1 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.