Heptranchias perlo

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) sHepPer1 3878.34 Gbp N/A 6.6 TiB
PacBio HiFi (.fq) sHepPer1 180.96 Gbp N/A 133.5 GiB
Arima sHepPer1 300.42 Gbp N/A 141.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 16 March 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
sHepPer1 PacBio HiFi (subreads) 3878.34 Gbp N/A 6.6 TiB
PacBio HiFi (.fq) 180.96 Gbp N/A 133.5 GiB
Arima 300.42 Gbp N/A 141.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 16 March 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 7 October 2023
sHepPer1.hap1.cur.20231007.fasta.gz (855.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 14 16.55 Mbp 2 172.36 Mbp
20 38 11.93 Mbp 4 141.86 Mbp
30 68 9.28 Mbp 7 101.16 Mbp
40 107 7.30 Mbp 11 83.46 Mbp
50 162 4.91 Mbp 15 66.82 Mbp
60 242 3.35 Mbp 20 53.47 Mbp
70 360 2.32 Mbp 27 42.91 Mbp
80 548 1.26 Mbp 36 28.33 Mbp
90 973 460.84 Kbp 66 3.08 Mbp
100 3713 6.69 Kbp 1879 6.69 Kbp
1.000x 3713 3.25 Gbp 1879 3.25 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 23 April 2024
sHepPer1.hap2.cur.20240423.fasta.gz (827.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 13 19.01 Mbp 2 175.37 Mbp
20 33 14.05 Mbp 4 140.88 Mbp
30 58 10.06 Mbp 7 100.62 Mbp
40 94 7.58 Mbp 10 87.73 Mbp
50 142 5.52 Mbp 14 71.73 Mbp
60 210 3.64 Mbp 18 62.30 Mbp
70 315 2.30 Mbp 24 51.69 Mbp
80 486 1.41 Mbp 31 37.16 Mbp
90 841 0.53 Mbp 43 17.07 Mbp
100 2914 9.87 Kbp 1143 9.87 Kbp
1.000x 2914 3.09 Gbp 1143 3.09 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 7 June 2023
sHepPer1.MT.20230607.fasta.gz (5.7 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/sHepPer1_hap1.yml (view)
species: Heptranchias perlo
specimen: sHepPer1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Heptranchias_perlo/sHepPer1/assembly_vgp_HiC_2.0/sHepPer1.HiC.hap1.20230606.fasta.gz
hap2: s3://genomeark/species/Heptranchias_perlo/sHepPer1/assembly_vgp_HiC_2.0/sHepPer1.HiC.hap2.20230606.fasta.gz
pretext_hap1: s3://genomeark/species/Heptranchias_perlo/sHepPer1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/sHepPer1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Heptranchias_perlo/sHepPer1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/sHepPer1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Heptranchias_perlo/sHepPer1/assembly_vgp_HiC_2.0/evaluation/merqury/sHepPer1_png/
mito: s3://genomeark/species/Heptranchias_perlo/sHepPer1/assembly_MT_rockefeller/sHepPer1.MT.20230607.fasta.gz
pacbio_read_dir: s3://genomeark/species/Heptranchias_perlo/sHepPer1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Heptranchias_perlo/sHepPer1/genomic_data/arima/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of sHepPer1, resulting in two complete haplotypes. This individual did have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The kmer spectra indicate a homogametic specimen. I am submitting both hap1 & hap2 for dual curation. This is the curation ticket for hap1. 
assembly_vgp_HiC_2.0/sHepPer1_hap2.yml (view)
species: Heptranchias perlo
specimen: sHepPer1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Heptranchias_perlo/sHepPer1/assembly_vgp_HiC_2.0/sHepPer1.HiC.hap1.20230606.fasta.gz
hap2: s3://genomeark/species/Heptranchias_perlo/sHepPer1/assembly_vgp_HiC_2.0/sHepPer1.HiC.hap2.20230606.fasta.gz
pretext_hap1: s3://genomeark/species/Heptranchias_perlo/sHepPer1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/sHepPer1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Heptranchias_perlo/sHepPer1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/sHepPer1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Heptranchias_perlo/sHepPer1/assembly_vgp_HiC_2.0/evaluation/merqury/sHepPer1_png/
mito: s3://genomeark/species/Heptranchias_perlo/sHepPer1/assembly_MT_rockefeller/sHepPer1.MT.20230607.fasta.gz
pacbio_read_dir: s3://genomeark/species/Heptranchias_perlo/sHepPer1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Heptranchias_perlo/sHepPer1/genomic_data/arima/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of sHepPer1, resulting in two complete haplotypes. This individual did have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The kmer spectra indicate a homogametic specimen. I am submitting both hap1 & hap2 for dual curation. This is the curation ticket for hap2. 
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.