Ophthalmolebias constanciae

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fOphCon1 104.36 Gbp N/A 45.1 GiB
PacBio HiFi (.bam) fOphCon1 109.17 Gbp N/A 354.6 GiB
Arima fOphCon1 87.34 Gbp N/A 47.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 7 July 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fOphCon1 PacBio HiFi (.fq) 104.36 Gbp N/A 45.1 GiB
PacBio HiFi (.bam) 109.17 Gbp N/A 354.6 GiB
Arima 87.34 Gbp N/A 47.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 7 July 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 17 June 2026
fOphCon1.hap1.cur.20260617.fasta.gz (478.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 11 13.61 Mbp 2 88.46 Mbp
20 26 11.28 Mbp 5 82.02 Mbp
30 45 9.57 Mbp 7 81.09 Mbp
40 67 7.88 Mbp 9 80.24 Mbp
50 93 6.72 Mbp 12 76.00 Mbp
60 124 5.47 Mbp 14 75.58 Mbp
70 166 3.90 Mbp 17 70.64 Mbp
80 226 2.67 Mbp 20 59.07 Mbp
90 317 1.57 Mbp 23 53.01 Mbp
100 1060 13.66 Kbp 570 13.66 Kbp
1.000x 1060 1.90 Gbp 570 1.90 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 17 June 2026
fOphCon1.hap2.cur.20260617.fasta.gz (417.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 10 15.43 Mbp 2 86.49 Mbp
20 24 11.23 Mbp 5 80.31 Mbp
30 42 9.51 Mbp 7 77.39 Mbp
40 62 8.03 Mbp 9 76.09 Mbp
50 88 6.35 Mbp 12 73.87 Mbp
60 120 4.65 Mbp 14 70.60 Mbp
70 166 3.38 Mbp 17 64.97 Mbp
80 228 2.39 Mbp 20 57.02 Mbp
90 324 1.39 Mbp 23 49.39 Mbp
100 866 15.70 Kbp 376 15.70 Kbp
1.000x 866 1.79 Gbp 376 1.79 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/fOphCon1.yml (view)
species: Ophthalmolebias constanciae
specimem: fOphCon1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Ophthalmolebias_constanciae/fOphCon1/assembly_vgp_HiC_2.0/fOphCon1.HiC.hap1.20251003.fasta.gz
hap2: s3://genomeark/species/Ophthalmolebias_constanciae/fOphCon1/assembly_vgp_HiC_2.0/fOphCon1.HiC.hap2.20251003.fasta.gz
pretext_hap1: s3://genomeark/species/Ophthalmolebias_constanciae/fOphCon1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fOphCon1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Ophthalmolebias_constanciae/fOphCon1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fOphCon1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Ophthalmolebias_constanciae/fOphCon1/assembly_vgp_HiC_2.0/evaluation/merqury/fOphCon1_png/
pacbio_read_dir: s3://genomeark/species/Ophthalmolebias_constanciae/fOphCon1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Ophthalmolebias_constanciae/fOphCon1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.12)
  - VGP8 HiC scaffolding workflow (v2.2) with mapq=10
  - VGP9 decontamination workflow unpublished using FCS (0.5.5+galaxy0) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of fOphCon1 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. A mitogenome could not be assembled, as no HiFi reads were mapped to the reference mitogenome.
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.