Carcharias taurus

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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_vgp_HiC_2.0 from 5 January 2024
sCarTau1.HiC.hap1.20240105.fasta.gz (1.3 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 14 24.10 Mbp 2 273.40 Mbp
20 39 16.60 Mbp 4 213.23 Mbp
30 74 11.87 Mbp 7 181.38 Mbp
40 120 9.18 Mbp 9 168.89 Mbp
50 180 6.91 Mbp 12 149.22 Mbp
60 263 4.84 Mbp 16 126.11 Mbp
70 382 3.29 Mbp 20 94.36 Mbp
80 570 1.98 Mbp 31 27.62 Mbp
90 915 0.91 Mbp 93 3.21 Mbp
100 3353 14.04 Kbp 1768 14.04 Kbp
1.000x 3353 4.81 Gbp 1768 4.82 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 5 January 2024
sCarTau1.HiC.hap2.20240105.fasta.gz (1.2 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 15 23.64 Mbp 2 229.18 Mbp
20 37 18.83 Mbp 4 201.17 Mbp
30 65 13.24 Mbp 7 168.02 Mbp
40 104 9.97 Mbp 10 159.68 Mbp
50 156 7.47 Mbp 12 147.31 Mbp
60 229 5.27 Mbp 16 123.91 Mbp
70 333 3.47 Mbp 19 113.32 Mbp
80 499 2.11 Mbp 25 49.96 Mbp
90 816 0.93 Mbp 53 4.09 Mbp
100 2705 11.83 Kbp 1233 11.83 Kbp
1.000x 2705 4.47 Gbp 1233 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.