Stegostoma tigrinum

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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

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) sSteFas4 153.76 Gbp N/A 123.1 GiB
Arima sSteFas4 316.14 Gbp N/A 150.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 27 September 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
sSteFas4 PacBio HiFi (.fq) 153.76 Gbp N/A 123.1 GiB
Arima 316.14 Gbp N/A 150.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 27 September 2024.
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 91 8.21 Mbp 10 96.42 Mbp
50 136 6.16 Mbp 14 79.02 Mbp
60 195 4.81 Mbp 19 62.29 Mbp
70 280 3.03 Mbp 25 51.52 Mbp
80 411 1.93 Mbp 31 41.83 Mbp
90 641 0.94 Mbp 43 16.79 Mbp
100 1994 7.96 Kbp 835 7.96 Kbp
1.000x 1994 3.18 Gbp 835 3.20 Gbp
NG based on genome size .
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 16 17.91 Mbp 2 166.56 Mbp
20 40 12.91 Mbp 5 114.86 Mbp
30 71 10.12 Mbp 9 102.24 Mbp
40 113 7.64 Mbp 12 82.41 Mbp
50 167 5.80 Mbp 17 68.03 Mbp
60 236 4.58 Mbp 23 59.48 Mbp
70 328 3.35 Mbp 30 49.85 Mbp
80 460 2.09 Mbp 39 31.85 Mbp
90 704 0.99 Mbp 75 4.56 Mbp
100 2136 13.88 Kbp 933 13.88 Kbp
1.000x 2136 3.59 Gbp 933 3.60 Gbp
NG based on genome size .
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.