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_curated from 11 May 2026
sEchCoo1.hap1.cur.20260511.fasta.gz (1.5 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 69 7.88 Mbp 3 256.62 Mbp
20 176 5.43 Mbp 6 232.41 Mbp
30 324 4.04 Mbp 9 192.08 Mbp
40 524 3.00 Mbp 13 160.87 Mbp
50 796 2.21 Mbp 18 114.76 Mbp
60 1157 1.66 Mbp 25 87.30 Mbp
70 1661 1.16 Mbp 34 62.73 Mbp
80 2397 0.76 Mbp 53 9.19 Mbp
90 3673 382.86 Kbp 366 1.06 Mbp
100 9058 2.67 Kbp 3905 8.81 Kbp
1.000x 9058 6.95 Gbp 3905 6.95 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 11 May 2026
sEchCoo1.hap2.cur.20260511.fasta.gz (1.2 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 62 7.65 Mbp 3 257.25 Mbp
20 157 5.45 Mbp 5 241.02 Mbp
30 284 4.22 Mbp 8 195.52 Mbp
40 453 3.10 Mbp 11 160.37 Mbp
50 685 2.28 Mbp 15 133.96 Mbp
60 994 1.71 Mbp 20 97.83 Mbp
70 1422 1.20 Mbp 27 79.65 Mbp
80 2049 0.78 Mbp 37 46.64 Mbp
90 3121 405.28 Kbp 75 3.58 Mbp
100 7129 838 bp 2205 9.08 Kbp
1.000x 7129 6.10 Gbp 2205 6.10 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.