Hiodon alosoides

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fHioAlo1 52.08 Gbp N/A 22.8 GiB
PacBio HiFi (.bam) fHioAlo1 52.24 Gbp N/A 172.9 GiB
Arima fHioAlo1 90.65 Gbp N/A 49.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 16 December 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fHioAlo1 PacBio HiFi (.fq) 52.08 Gbp N/A 22.8 GiB
PacBio HiFi (.bam) 52.24 Gbp N/A 172.9 GiB
Arima 90.65 Gbp N/A 49.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 16 December 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 2 February 2026
fHioAlo1.HiC.hap1.20260202.fasta.gz (194.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 32.76 Mbp 2 48.97 Mbp
20 5 28.29 Mbp 4 43.59 Mbp
30 8 22.79 Mbp 6 36.13 Mbp
40 12 18.15 Mbp 8 33.91 Mbp
50 17 15.03 Mbp 11 29.81 Mbp
60 23 13.10 Mbp 14 26.89 Mbp
70 31 9.32 Mbp 17 25.82 Mbp
80 45 4.11 Mbp 20 23.95 Mbp
90 85 1.22 Mbp 24 18.05 Mbp
100 439 9.33 Kbp 337 9.33 Kbp
1.000x 439 0.82 Gbp 337 0.82 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 2 February 2026
fHioAlo1.HiC.hap2.20260202.fasta.gz (200.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 39.40 Mbp 2 45.28 Mbp
20 5 26.56 Mbp 4 37.37 Mbp
30 9 22.01 Mbp 7 36.10 Mbp
40 14 17.59 Mbp 9 32.30 Mbp
50 19 15.29 Mbp 12 30.26 Mbp
60 25 10.87 Mbp 15 27.41 Mbp
70 35 6.26 Mbp 18 24.99 Mbp
80 52 3.40 Mbp 22 23.43 Mbp
90 100 1.05 Mbp 29 1.44 Mbp
100 417 9.61 Kbp 329 9.61 Kbp
1.000x 417 0.86 Gbp 329 0.86 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 2 February 2026
fHioAlo1.MT.20260202.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fHioAlo1.yml (view)
species: Hiodon alosoides
specimem: fHioAlo1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Hiodon_alosoides/fHioAlo1/assembly_vgp_HiC_2.0/fHioAlo1.HiC.hap1.20260202.fasta.gz
hap2: s3://genomeark/species/Hiodon_alosoides/fHioAlo1/assembly_vgp_HiC_2.0/fHioAlo1.HiC.hap2.20260202.fasta.gz
pretext_hap1: s3://genomeark/species/Hiodon_alosoides/fHioAlo1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fHioAlo1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Hiodon_alosoides/fHioAlo1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fHioAlo1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Hiodon_alosoides/fHioAlo1/assembly_vgp_HiC_2.0/evaluation/merqury/fHioAlo1_png/
pacbio_read_dir: s3://genomeark/species/Hiodon_alosoides/fHioAlo1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Hiodon_alosoides/fHioAlo1/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 fHioAlo1 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.