Albula glossodonta

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fAlbGlo1 68.36 Gbp N/A 31.4 GiB
PacBio HiFi (.bam) fAlbGlo1 69.82 Gbp N/A 232.6 GiB
Arima fAlbGlo1 109.90 Gbp N/A 60.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 6 November 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fAlbGlo1 PacBio HiFi (.fq) 68.36 Gbp N/A 31.4 GiB
PacBio HiFi (.bam) 69.82 Gbp N/A 232.6 GiB
Arima 109.90 Gbp N/A 60.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 6 November 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 14 November 2025
fAlbGlo1.HiC.hap1.20251114.fasta.gz (255.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 43.18 Mbp 2 72.92 Mbp
20 5 41.80 Mbp 3 57.25 Mbp
30 7 39.13 Mbp 5 46.97 Mbp
40 10 36.72 Mbp 7 42.45 Mbp
50 13 31.10 Mbp 10 40.58 Mbp
60 16 27.73 Mbp 12 38.15 Mbp
70 20 26.64 Mbp 15 37.77 Mbp
80 24 23.34 Mbp 18 30.59 Mbp
90 30 5.85 Mbp 21 27.85 Mbp
100 211 6.87 Kbp 149 6.87 Kbp
1.000x 211 0.99 Gbp 149 0.99 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 14 November 2025
fAlbGlo1.HiC.hap2.20251114.fasta.gz (255.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 52.39 Mbp 2 65.74 Mbp
20 4 43.31 Mbp 3 57.05 Mbp
30 6 40.38 Mbp 5 47.89 Mbp
40 9 37.30 Mbp 8 42.47 Mbp
50 12 36.50 Mbp 10 41.54 Mbp
60 15 29.78 Mbp 12 40.38 Mbp
70 18 27.19 Mbp 15 36.19 Mbp
80 22 21.62 Mbp 18 31.13 Mbp
90 27 12.07 Mbp 21 28.00 Mbp
100 145 6.87 Kbp 90 6.87 Kbp
1.000x 145 0.98 Gbp 90 0.98 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 13 November 2025
fAlbGlo1.MT.20251113.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fAlbGlo1.yml (view)
species: Albula glossodonta
specimem: fAlbGlo1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Albula_glossodonta/fAlbGlo1/assembly_vgp_HiC_2.0/fAlbGlo1.HiC.hap1.20251114.fasta.gz
hap2: s3://genomeark/species/Albula_glossodonta/fAlbGlo1/assembly_vgp_HiC_2.0/fAlbGlo1.HiC.hap2.20251114.fasta.gz
pretext_hap1: s3://genomeark/species/Albula_glossodonta/fAlbGlo1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fAlbGlo1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Albula_glossodonta/fAlbGlo1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fAlbGlo1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Albula_glossodonta/fAlbGlo1/assembly_vgp_HiC_2.0/evaluation/merqury/fAlbGlo1_png/
pacbio_read_dir: s3://genomeark/species/Albula_glossodonta/fAlbGlo1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Albula_glossodonta/fAlbGlo1/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 (v0.4)
  - VGP8 HiC scaffolding workflow (v3.2) with mapq=10
  - VGP9 decontamination workflow (v1.2) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of fAlbGlo1 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.