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 30 January 2026
kcIchGage1.HiC.hap1.20260130.fasta.gz (266.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 7 15.01 Mbp 3 34.00 Mbp
20 16 12.76 Mbp 8 18.10 Mbp
30 28 9.01 Mbp 15 16.72 Mbp
40 42 6.95 Mbp 22 15.06 Mbp
50 63 4.70 Mbp 31 14.12 Mbp
60 96 2.74 Mbp 39 13.25 Mbp
70 152 1.56 Mbp 49 11.54 Mbp
80 266 0.70 Mbp 60 8.98 Mbp
90 547 258.62 Kbp 96 0.79 Mbp
100 1715 5.07 Kbp 972 5.07 Kbp
1.000x 1715 1.18 Gbp 972 1.18 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 30 January 2026
kcIchGage1.HiC.hap2.20260130.fasta.gz (284.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 8 14.82 Mbp 4 28.07 Mbp
20 17 12.22 Mbp 10 18.09 Mbp
30 29 9.66 Mbp 17 16.21 Mbp
40 45 7.30 Mbp 26 14.74 Mbp
50 65 5.20 Mbp 35 14.01 Mbp
60 102 2.56 Mbp 45 11.95 Mbp
70 175 1.27 Mbp 57 9.99 Mbp
80 326 0.59 Mbp 72 6.67 Mbp
90 693 229.60 Kbp 161 455.62 Kbp
100 2004 8.04 Kbp 1086 8.04 Kbp
1.000x 2004 1.31 Gbp 1086 1.31 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 31 January 2026
kcIchGage1.MT.20260131.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
gametic/assembly_vgp_HiC_2.0/kcIchGage1.yml (view)
species: Ichthyomyzon gagei
specimem: kcIchGage1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Ichthyomyzon_gagei/kcIchGage1/gametic/assembly_vgp_HiC_2.0/kcIchGage1.HiC.hap1.20260130.fasta.gz
hap2: s3://genomeark/species/Ichthyomyzon_gagei/kcIchGage1/gametic/assembly_vgp_HiC_2.0/kcIchGage1.HiC.hap2.20260130.fasta.gz
pretext_hap1: s3://genomeark/species/Ichthyomyzon_gagei/kcIchGage1/gametic/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/kcIchGage1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Ichthyomyzon_gagei/kcIchGage1/gametic/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/kcIchGage1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Ichthyomyzon_gagei/kcIchGage1/gametic/assembly_vgp_HiC_2.0/evaluation/merqury/kcIchGage1_png/
pacbio_read_dir: s3://genomeark/species/Ichthyomyzon_gagei/kcIchGage1/gametic/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Ichthyomyzon_gagei/kcIchGage1/gametic/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 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. The mitoHiFi assembly is about three times the expected length and contains 81 annotated genes. Self-alignment of the mito-assembly in NCBI suggests that about three mitogenomes were assembled into a single contig. Therefore, the assembly was trimmed to retain only the 2nd part and re-annotated using MITOS2 on galaxy.
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.