Heterodontus francisci

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) sHetFra1 215.55 Gbp N/A 160.1 GiB
Arima sHetFra1 642.00 Gbp N/A 301.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 27 February 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
sHetFra1 PacBio HiFi (.fq) 215.55 Gbp N/A 160.1 GiB
Arima 642.00 Gbp N/A 301.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 27 February 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 9 January 2024
sHetFra1.hap1.cur.20240109.fasta.gz (1.4 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 47 10.00 Mbp 3 214.64 Mbp
20 120 7.03 Mbp 6 163.05 Mbp
30 217 5.55 Mbp 10 126.46 Mbp
40 341 4.22 Mbp 15 107.91 Mbp
50 500 3.42 Mbp 21 90.14 Mbp
60 704 2.60 Mbp 29 74.47 Mbp
70 975 1.89 Mbp 39 44.09 Mbp
80 1360 1.25 Mbp 77 7.53 Mbp
90 1993 0.70 Mbp 246 2.08 Mbp
100 5087 13.35 Kbp 2306 13.35 Kbp
1.000x 5087 5.98 Gbp 2306 6.01 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 9 January 2024
sHetFra1.hap2.cur.20240109.fasta.gz (1.3 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 42 9.55 Mbp 2 232.73 Mbp
20 106 6.85 Mbp 5 208.07 Mbp
30 192 5.41 Mbp 8 129.45 Mbp
40 300 4.21 Mbp 13 119.98 Mbp
50 435 3.49 Mbp 17 97.90 Mbp
60 610 2.52 Mbp 23 78.62 Mbp
70 855 1.79 Mbp 31 62.63 Mbp
80 1213 1.17 Mbp 41 35.59 Mbp
90 1802 0.64 Mbp 97 3.28 Mbp
100 4286 13.81 Kbp 1496 13.81 Kbp
1.000x 4286 5.17 Gbp 1496 5.20 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 6 January 2024
sHetFra1.MT.20240106.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/sHetFra1_hap1.yml (view)
species: Heterodontus francisci
specimen: sHetFra1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Heterodontus_francisci/sHetFra1/assembly_vgp_HiC_2.0/sHetFra1.HiC.hap1.20230522.fasta.gz
hap2: s3://genomeark/species/Heterodontus_francisci/sHetFra1/assembly_vgp_HiC_2.0/sHetFra1.HiC.hap2.20230522.fasta.gz
pretext_hap1: s3://genomeark/species/Heterodontus_francisci/sHetFra1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/sHetFra1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Heterodontus_francisci/sHetFra1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/sHetFra1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Heterodontus_francisci/sHetFra1/assembly_vgp_HiC_2.0/evaluation/merqury/sHetFra1_png/
pacbio_read_dir: s3://genomeark/species/Heterodontus_francisci/sHetFra1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Heterodontus_francisci/sHetFra1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Heterodontus_francisci/sHetFra1/genomic_data/arima/
pipeline:
  - hifiasm (0.18.8+galaxy1)
  - solve (3.7)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of sHetFra1, resulting in two complete haplotypes. This individual did have bionano data. Bionano Solve 3.7 was run with No Filter for the genome maps conflict and sequence conflict filter. 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/sHetFra1_hap2.yml (view)
species: Heterodontus francisci
specimen: sHetFra1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Heterodontus_francisci/sHetFra1/assembly_vgp_HiC_2.0/sHetFra1.HiC.hap1.20230522.fasta.gz
hap2: s3://genomeark/species/Heterodontus_francisci/sHetFra1/assembly_vgp_HiC_2.0/sHetFra1.HiC.hap2.20230522.fasta.gz
pretext_hap1: s3://genomeark/species/Heterodontus_francisci/sHetFra1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/sHetFra1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Heterodontus_francisci/sHetFra1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/sHetFra1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Heterodontus_francisci/sHetFra1/assembly_vgp_HiC_2.0/evaluation/merqury/sHetFra1_png/
pacbio_read_dir: s3://genomeark/species/Heterodontus_francisci/sHetFra1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Heterodontus_francisci/sHetFra1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Heterodontus_francisci/sHetFra1/genomic_data/arima/
pipeline:
  - hifiasm (0.18.8+galaxy1)
  - solve (3.7)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of sHetFra1, resulting in two complete haplotypes. This individual did have bionano data. Bionano Solve 3.7 was run with No Filter for the genome maps conflict and sequence conflict filter. 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.