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_vgp_HiC_2.0 from 3 October 2025
fOphCon1.HiC.hap1.20251003.fasta.gz (433.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 10 15.49 Mbp 2 126.87 Mbp
20 25 11.41 Mbp 3 103.69 Mbp
30 44 9.66 Mbp 6 82.02 Mbp
40 65 8.21 Mbp 8 80.24 Mbp
50 91 6.79 Mbp 10 78.08 Mbp
60 122 5.48 Mbp 13 75.24 Mbp
70 163 3.98 Mbp 15 73.12 Mbp
80 223 2.69 Mbp 18 61.98 Mbp
90 313 1.58 Mbp 21 56.93 Mbp
100 1057 9.81 Kbp 576 9.81 Kbp
1.000x 1057 1.90 Gbp 576 1.90 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 3 October 2025
fOphCon1.HiC.hap2.20251003.fasta.gz (417.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 10 15.29 Mbp 2 118.53 Mbp
20 24 11.35 Mbp 3 107.45 Mbp
30 42 9.60 Mbp 5 98.70 Mbp
40 62 8.21 Mbp 7 85.04 Mbp
50 87 6.37 Mbp 9 79.02 Mbp
60 118 4.72 Mbp 12 72.76 Mbp
70 163 3.46 Mbp 14 69.88 Mbp
80 223 2.52 Mbp 17 57.02 Mbp
90 317 1.43 Mbp 21 23.63 Mbp
100 857 15.70 Kbp 393 15.70 Kbp
1.000x 857 1.79 Gbp 393 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.