Carcharias taurus

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CC BY-NC-SA 2.0 John Turnbull (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) sCarTau1 3916.08 Gbp N/A 6.6 TiB
PacBio HiFi (.fq) sCarTau1 199.77 Gbp N/A 160.9 GiB
PacBio HiFi (.bam) sCarTau1 623.69 Gbp N/A 2.1 TiB
Arima sCarTau1 334.98 Gbp N/A 160.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
sCarTau1 PacBio HiFi (subreads) 3916.08 Gbp N/A 6.6 TiB
PacBio HiFi (.fq) 199.77 Gbp N/A 160.9 GiB
PacBio HiFi (.bam) 623.69 Gbp N/A 2.1 TiB
Arima 334.98 Gbp N/A 160.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 June 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 23 January 2026
sCarTau1.hap1.cur.20260123.fasta.gz (1.3 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 15 23.64 Mbp 2 232.64 Mbp
20 39 17.80 Mbp 5 198.81 Mbp
30 73 12.77 Mbp 7 169.37 Mbp
40 116 9.62 Mbp 10 163.20 Mbp
50 174 7.02 Mbp 13 148.99 Mbp
60 256 4.96 Mbp 17 126.11 Mbp
70 374 3.30 Mbp 21 114.37 Mbp
80 558 2.03 Mbp 29 34.58 Mbp
90 898 0.94 Mbp 67 4.33 Mbp
100 3354 14.04 Kbp 1711 14.04 Kbp
1.000x 3354 4.80 Gbp 1711 4.81 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 23 January 2026
sCarTau1.hap2.cur.20260123.fasta.gz (1.2 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 14 23.86 Mbp 2 231.74 Mbp
20 36 18.00 Mbp 4 207.14 Mbp
30 66 12.18 Mbp 7 170.40 Mbp
40 108 9.25 Mbp 9 163.14 Mbp
50 162 7.25 Mbp 12 148.96 Mbp
60 235 5.24 Mbp 15 141.78 Mbp
70 341 3.40 Mbp 19 122.34 Mbp
80 512 2.08 Mbp 23 65.21 Mbp
90 834 0.91 Mbp 36 17.87 Mbp
100 2705 11.83 Kbp 1171 11.83 Kbp
1.000x 2705 4.47 Gbp 1171 4.48 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 5 January 2024
sCarTau1.MT.20240105.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/sCarTau1.yml (view)
species: Carcharias taurus
specimen: sCarTau1
projects: 
  - vgp
data_location: S3
release_to: S3
hap1: s3://genomeark/species/Carcharias_taurus/sCarTau1/assembly_vgp_HiC_2.0/sCarTau1.HiC.hap1.20240105.fasta.gz
hap2: s3://genomeark/species/Carcharias_taurus/sCarTau1/assembly_vgp_HiC_2.0/sCarTau1.HiC.hap2.20240105.fasta.gz
pretext_hap1: s3://genomeark/species/Carcharias_taurus/sCarTau1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/sCarTau1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Carcharias_taurus/sCarTau1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/sCarTau1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Carcharias_taurus/sCarTau1/assembly_vgp_HiC_2.0/evaluation/merqury/sCarTau1_png/
pacbio_read_dir: s3://genomeark/species/Carcharias_taurus/sCarTau1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Carcharias_taurus/sCarTau1/genomic_data/arima/
mito: s3://genomeark/species/Carcharias_taurus/sCarTau1/assembly_MT_rockefeller/sCarTau1.MT.20240105.fasta.gz
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - solve (3.7)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of sCarTau1, resulting in two complete haplotypes. This individual did have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. 
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.