Pristiophorus japonicus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) sPriJap1 277.97 Gbp N/A 128.5 GiB
PacBio HiFi (.bam) sPriJap1 279.69 Gbp N/A 1.1 TiB
Arima sPriJap1 456.02 Gbp N/A 234.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 21 May 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
sPriJap1 PacBio HiFi (.fq) 277.97 Gbp N/A 128.5 GiB
PacBio HiFi (.bam) 279.69 Gbp N/A 1.1 TiB
Arima 456.02 Gbp N/A 234.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 21 May 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 10 October 2024
sPriJap1.hap1.cur.20241010.fasta.gz (1.4 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 73 6.07 Mbp 2 375.65 Mbp
20 193 4.10 Mbp 3 331.97 Mbp
30 361 3.12 Mbp 5 307.09 Mbp
40 576 2.42 Mbp 7 252.57 Mbp
50 853 1.89 Mbp 10 225.85 Mbp
60 1218 1.40 Mbp 13 196.98 Mbp
70 1717 1.00 Mbp 16 138.63 Mbp
80 2427 0.68 Mbp 21 95.32 Mbp
90 3631 338.55 Kbp 50 4.54 Mbp
100 10302 2.40 Kbp 4317 2.40 Kbp
1.000x 10302 5.92 Gbp 4317 5.92 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 10 October 2024
sPriJap1.hap2.cur.20241010.fasta.gz (1.6 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 80 5.97 Mbp 2 373.66 Mbp
20 211 4.13 Mbp 4 311.59 Mbp
30 389 3.13 Mbp 6 257.41 Mbp
40 623 2.37 Mbp 8 249.31 Mbp
50 930 1.80 Mbp 11 223.62 Mbp
60 1338 1.35 Mbp 14 188.65 Mbp
70 1893 0.97 Mbp 18 114.62 Mbp
80 2707 0.62 Mbp 34 11.03 Mbp
90 4154 298.67 Kbp 312 0.98 Mbp
100 11579 1 bp 5626 4.06 Kbp
1.000x 11579 6.36 Gbp 5626 6.37 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/sPriJap1.yml (view)
species: Pristiophorus japonicus
specimen: sPriJap1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Pristiophorus_japonicus/sPriJap1/assembly_vgp_HiC_2.0/sPriJap1.HiC.hap1.20240604.fasta.gz
hap2: s3://genomeark/species/Pristiophorus_japonicus/sPriJap1/assembly_vgp_HiC_2.0/sPriJap1.HiC.hap2.20240604.fasta.gz
pretext_hap1: s3://genomeark/species/Pristiophorus_japonicus/sPriJap1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/sPriJap1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Pristiophorus_japonicus/sPriJap1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/sPriJap1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Pristiophorus_japonicus/sPriJap1/assembly_vgp_HiC_2.0/evaluation/merqury/hap1_purged/sPriJap1_png/
pacbio_read_dir: s3://genomeark/species/Pristiophorus_japonicus/sPriJap1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Pristiophorus_japonicus/sPriJap1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - purge_dups (1.2.6+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of sPriJap1, resulting in two complete haplotypes. The contigs each underwent purge_dups, with the BED file modified to not remove contigs marked as REPEAT. HiC scaffolding was performed with YaHS. The HiC prep kit used was Arima library prep. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. This is a VGP Phase 1 species we are submitting for dual curation. Hap2 has a larger assembly size (6.43Gbp) compared to hap1 (5.86Gbp), which is likely made up of repeats that weren't placed by scaffolding. Repeat masking (using a library generated from RepeatModeler on hap2) results in 71.67% of hap2 being masked. 
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.