Echinorhinus cookei

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) sEchCoo1 378.22 Gbp N/A 170.6 GiB
PacBio HiFi (.bam) sEchCoo1 408.28 Gbp N/A 1.3 TiB
Arima sEchCoo1 489.43 Gbp N/A 257.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 5 January 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
sEchCoo1 PacBio HiFi (.fq) 378.22 Gbp N/A 170.6 GiB
PacBio HiFi (.bam) 408.28 Gbp N/A 1.3 TiB
Arima 489.43 Gbp N/A 257.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 5 January 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 6 April 2026
sEchCoo1.HiC.hap1.20260406.fasta.gz (1.3 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 70 7.88 Mbp 3 239.02 Mbp
20 177 5.58 Mbp 6 231.95 Mbp
30 325 4.14 Mbp 10 164.15 Mbp
40 525 3.03 Mbp 14 140.36 Mbp
50 797 2.27 Mbp 20 100.32 Mbp
60 1156 1.70 Mbp 29 69.85 Mbp
70 1659 1.18 Mbp 43 30.89 Mbp
80 2395 0.77 Mbp 135 4.01 Mbp
90 3674 386.17 Kbp 515 1.03 Mbp
100 9205 8.81 Kbp 4233 8.81 Kbp
1.000x 9205 7.07 Gbp 4233 7.07 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 6 April 2026
sEchCoo1.HiC.hap2.20260406.fasta.gz (1.2 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 61 7.57 Mbp 2 257.25 Mbp
20 157 5.37 Mbp 4 237.65 Mbp
30 284 4.14 Mbp 7 188.57 Mbp
40 453 3.06 Mbp 10 157.69 Mbp
50 686 2.23 Mbp 15 129.23 Mbp
60 998 1.67 Mbp 20 96.10 Mbp
70 1429 1.18 Mbp 27 75.95 Mbp
80 2058 0.77 Mbp 38 32.96 Mbp
90 3130 399.40 Kbp 126 2.24 Mbp
100 7074 9.08 Kbp 2282 9.08 Kbp
1.000x 7074 6.02 Gbp 2282 6.02 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 6 April 2026
sEchCoo1.MT.20260406.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/sEchCoo1.yml (view)
species: Echinorhinus cookei
specimem: sEchCoo1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Echinorhinus_cookei/sEchCoo1/assembly_vgp_HiC_2.0/sEchCoo1.HiC.hap1.20260406.fasta.gz
hap2: s3://genomeark/species/Echinorhinus_cookei/sEchCoo1/assembly_vgp_HiC_2.0/sEchCoo1.HiC.hap2.20260406.fasta.gz
pretext_hap1: s3://genomeark/species/Echinorhinus_cookei/sEchCoo1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/sEchCoo1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Echinorhinus_cookei/sEchCoo1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/sEchCoo1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Echinorhinus_cookei/sEchCoo1/assembly_vgp_HiC_2.0/evaluation/merqury/sEchCoo1_png/
pacbio_read_dir: s3://genomeark/species/Echinorhinus_cookei/sEchCoo1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Echinorhinus_cookei/sEchCoo1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy3)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.8)
  - VGP4 HiFi HiC assembly workflow (v0.6)
  - VGP8 HiC scaffolding workflow (v3.4) with mapq=10. Note that in the VGP8 v3.4 workflow, the HiC duplicates were not removed because the -r flag was not on in samtools markdup tool (even if the workflow says it’s removed).
  - VGP9 decontamination workflow (v1.3) 
  - VGP6b purging hap1 (v0.8.5)
  - Pre-curation worklfow (v20260330 github update) with mapq=10, remove HiC duplicates and generate high-resolution map
notes: This was a Hifiasm-HiC assembly of sEchCoo1 resulting in two haplotype assemblies. HiC data were generated using the Arima library prep kit, and require trimming the first 5 bp off from the 5' end of both read files. The restriction enzymes used were the Arima v2 kit, so the cutting sites are GATC, GANTC, CTNAG, TTAA.
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.