Coregonus huntsmani

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CC BY 4.0 Ian Manning (iNaturalist)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) fCorHun2 1062.91 Gbp N/A 1.8 TiB
PacBio HiFi (.fq) fCorHun2 154.75 Gbp N/A 75.3 GiB
PacBio HiFi (.bam) fCorHun2 315.95 Gbp N/A 414.4 GiB
Arima fCorHun2 264.04 Gbp N/A 138.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 3 September 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fCorHun2 PacBio HiFi (subreads) 1062.91 Gbp N/A 1.8 TiB
PacBio HiFi (.fq) 154.75 Gbp N/A 75.3 GiB
PacBio HiFi (.bam) 315.95 Gbp N/A 414.4 GiB
Arima 264.04 Gbp N/A 138.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 3 September 2025.
Assemblies
Individual 2 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 22 September 2025
fCorHun2.HiC.hap1.20250922.fasta.gz (534.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 20 7.87 Mbp 2 161.07 Mbp
20 56 5.05 Mbp 3 121.37 Mbp
30 110 3.49 Mbp 5 98.92 Mbp
40 184 2.63 Mbp 8 78.93 Mbp
50 280 1.97 Mbp 11 58.17 Mbp
60 412 1.40 Mbp 15 47.91 Mbp
70 604 0.93 Mbp 20 44.83 Mbp
80 906 0.57 Mbp 25 39.81 Mbp
90 1454 282.22 Kbp 55 1.63 Mbp
100 3657 5.91 Kbp 1383 5.91 Kbp
1.000x 3657 2.20 Gbp 1383 2.20 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 22 September 2025
fCorHun2.HiC.hap2.20250922.fasta.gz (600.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 13 15.64 Mbp 1 257.92 Mbp
20 32 11.08 Mbp 3 141.56 Mbp
30 57 8.44 Mbp 5 116.49 Mbp
40 93 5.26 Mbp 9 63.18 Mbp
50 153 3.38 Mbp 13 55.68 Mbp
60 247 2.23 Mbp 17 54.23 Mbp
70 395 1.30 Mbp 22 50.46 Mbp
80 659 0.70 Mbp 27 49.07 Mbp
90 1180 321.60 Kbp 33 33.48 Mbp
100 3509 6.18 Kbp 993 6.18 Kbp
1.000x 3509 2.51 Gbp 993 2.51 Gbp
NG based on genome size .
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 22 September 2025
fCorHun2.MT.20250922.fasta.gz (5.5 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fCorHun2.yml (view)
species: Coregonus huntsmani
specimem: fCorHun2
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Coregonus_huntsmani/fCorHun2/assembly_vgp_HiC_2.0/fCorHun2.HiC.hap1.20250922.fasta.gz
hap2: s3://genomeark/species/Coregonus_huntsmani/fCorHun2/assembly_vgp_HiC_2.0/fCorHun2.HiC.hap2.20250922.fasta.gz
pretext_hap1: s3://genomeark/species/Coregonus_huntsmani/fCorHun2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fCorHun2_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Coregonus_huntsmani/fCorHun2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fCorHun2_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Coregonus_huntsmani/fCorHun2/assembly_vgp_HiC_2.0/evaluation/merqury/fCorHun2_png/
pacbio_read_dir: s3://genomeark/species/Coregonus_huntsmani/fCorHun2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Coregonus_huntsmani/fCorHun2/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.11)
  - VGP8 HiC scaffolding workflow (v2.2) with mapq=10
  - VGP9 decontamination workflow (unpublished) using FCS (v0.5.5+galaxy0)
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of fCorHun2 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.