Stegostoma fasciatum

zebra shark

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Resource Primary Assembly Alternate Assembly
GenBank sSteFas1: GCA_022316705.1
ENA sSteFas1: GCA_022316705.1
UCSC Genome Browser sSteFas1: GCA_022316705.1

metadata.yaml (view) (edit on github)
species:
  common_name: zebra shark
  name: Stegostoma fasciatum
  short_name: sSteFas
  taxon_id: 378071
  order:
    name: Orectolobiformes
  family:
    name: Stegostomatidae
  individuals:
  - short_name: sSteFas4
  genome_size: 3157655626
  genome_size_method: 
  project: [ ]
No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) sSteFas4 153.76 Gbp 48.69x 123.1 GiB
Arima sSteFas4 316.14 Gbp 100.12x 150.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.16 Gbp.
Last upload on 27 June 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
sSteFas4 PacBio HiFi (.fq) 153.76 Gbp 48.69x 123.1 GiB
Arima 316.14 Gbp 100.12x 150.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.16 Gbp.
Last upload on 27 June 2023.
Assemblies
Individual 4 Haplotype 1 Assembly
Version assembly_curated from 25 April 2023
sSteFas4.hap1.cur.20230425.fasta.gz (887.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 13 20.09 Mbp 2 163.09 Mbp
20 32 15.30 Mbp 5 130.64 Mbp
30 57 10.71 Mbp 7 108.38 Mbp
40 90 8.24 Mbp 10 96.42 Mbp
50 134 6.24 Mbp 14 79.02 Mbp
60 192 4.83 Mbp 19 62.29 Mbp
70 274 3.12 Mbp 24 54.41 Mbp
80 402 2.01 Mbp 31 41.83 Mbp
90 619 1.00 Mbp 41 19.65 Mbp
100 1447 81.51 Kbp 250 267.03 Kbp
1.008x 1994 3.18 Gbp 835 3.20 Gbp
NG based on genome size 3.16 Gbp.
Individual 4 Haplotype 2 Assembly
Version assembly_curated from 25 April 2023
sSteFas4.hap2.decon.20230425.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 14 18.32 Mbp 2 166.56 Mbp
20 33 14.52 Mbp 4 135.01 Mbp
30 59 10.91 Mbp 7 105.49 Mbp
40 91 8.61 Mbp 10 98.61 Mbp
50 132 6.87 Mbp 14 77.54 Mbp
60 184 5.39 Mbp 19 62.32 Mbp
70 249 4.44 Mbp 24 58.53 Mbp
80 332 3.32 Mbp 30 49.85 Mbp
90 445 2.24 Mbp 37 34.66 Mbp
100 637 1.24 Mbp 59 6.59 Mbp
1.137x 2136 3.59 Gbp 933 3.60 Gbp
NG based on genome size 3.16 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/sSteFas4.yml (view)
species: Stegostoma fasciatum
specimen: sSteFas4
projects: 
  - vgp
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Stegostoma_fasciatum/sSteFas4/assembly_vgp_HiC_2.0/sSteFas4.HiC.hap1.20221121.fasta.gz
hap2: s3://genomeark/species/Stegostoma_fasciatum/sSteFas4/assembly_vgp_HiC_2.0/sSteFas4.HiC.hap2.20221121.fasta.gz
pretext_hap1: s3://genomeark/species/Stegostoma_fasciatum/sSteFas4/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/sSteFas4_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Stegostoma_fasciatum/sSteFas4/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/sSteFas4_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Stegostoma_fasciatum/sSteFas4/assembly_vgp_HiC_2.0/evaluation/merqury/sSteFas4_png/
pacbio_read_dir: s3://genomeark/species/Stegostoma_fasciatum/sSteFas4/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Stegostoma_fasciatum/sSteFas4/genomic_data/arima/
pipeline:
  - hifiasm (0.16.1+galaxy3)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of sSteFas4 (VGL ID: sSteTig2), resulting in two complete haplotypes. This individual did not have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The kmer spectra indicates a homogametic specimen. We are submitting haplotype 1 for curation.
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.