Ichthyomyzon gagei

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
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
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 19 December 2025
kcIchGage1.HiC.hap1.20251219.fasta.gz (281.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 8 14.73 Mbp 5 20.66 Mbp
20 18 11.94 Mbp 12 17.82 Mbp
30 30 9.66 Mbp 20 15.60 Mbp
40 45 7.35 Mbp 28 14.34 Mbp
50 67 4.96 Mbp 37 13.82 Mbp
60 104 2.80 Mbp 47 11.79 Mbp
70 174 1.22 Mbp 59 9.54 Mbp
80 321 0.61 Mbp 76 5.01 Mbp
90 665 247.76 Kbp 225 386.99 Kbp
100 2000 5.09 Kbp 1298 5.09 Kbp
1.000x 2000 1.28 Gbp 1298 1.28 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 19 December 2025
kcIchGage1.HiC.hap2.20251219.fasta.gz (268.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 8 14.50 Mbp 4 26.93 Mbp
20 17 11.91 Mbp 10 17.91 Mbp
30 28 9.23 Mbp 17 16.03 Mbp
40 42 7.14 Mbp 25 15.00 Mbp
50 61 5.41 Mbp 33 13.92 Mbp
60 88 3.37 Mbp 42 13.17 Mbp
70 131 2.15 Mbp 51 11.44 Mbp
80 221 0.90 Mbp 63 9.06 Mbp
90 443 315.34 Kbp 90 1.01 Mbp
100 1473 8.59 Kbp 857 8.59 Kbp
1.000x 1473 1.18 Gbp 857 1.18 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 19 December 2025
kcIchGage1.MT.20251219.fasta.gz (5.1 KiB)

Quality: not computed
Assembly Metadata
somatic/assembly_vgp_HiC_2.0/kcIchGage1.yml (view)
species: Ichthyomyzon gagei
specimem: kcIchGage1 (somatic)
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Ichthyomyzon_gagei/kcIchGage1/somatic/assembly_vgp_HiC_2.0/kcIchGage1.HiC.hap1.20251219.fasta.gz
hap2: s3://genomeark/species/Ichthyomyzon_gagei/kcIchGage1/somatic/assembly_vgp_HiC_2.0/kcIchGage1.HiC.hap2.20251219.fasta.gz
pretext_hap1: s3://genomeark/species/Ichthyomyzon_gagei/kcIchGage1/somatic/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/kcIchGage1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Ichthyomyzon_gagei/kcIchGage1/somatic/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/kcIchGage1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Ichthyomyzon_gagei/kcIchGage1/somatic/assembly_vgp_HiC_2.0/evaluation/merqury/kcIchGage1_png/
pacbio_read_dir: s3://genomeark/species/Ichthyomyzon_gagei/kcIchGage1/somatic/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Ichthyomyzon_gagei/kcIchGage1/somatic/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.6)
  - VGP4 HiFi HiC assembly workflow (v0.5)
  - VGP8 HiC scaffolding workflow (v3.3) with mapq=10
  - VGP9 decontamination workflow (v1.2) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of kcIchGage1 (somatic) 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.