Alepocephalus tenebrosus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fAleTen1 48.40 Gbp N/A 21.3 GiB
PacBio HiFi (.bam) fAleTen1 49.12 Gbp N/A 163.3 GiB
Arima fAleTen1 82.39 Gbp N/A 45.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 November 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fAleTen1 PacBio HiFi (.fq) 48.40 Gbp N/A 21.3 GiB
PacBio HiFi (.bam) 49.12 Gbp N/A 163.3 GiB
Arima 82.39 Gbp N/A 45.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 November 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 2 December 2025
fAleTen1.HiC.hap1.20251202.fasta.gz (519.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 61 2.54 Mbp 1 359.80 Mbp
20 163 1.66 Mbp 2 200.39 Mbp
30 304 1.28 Mbp 3 195.55 Mbp
40 492 0.96 Mbp 4 178.04 Mbp
50 738 0.74 Mbp 5 175.71 Mbp
60 1065 0.54 Mbp 6 174.80 Mbp
70 1518 381.23 Kbp 7 166.96 Mbp
80 2204 236.29 Kbp 9 118.21 Mbp
90 3435 118.21 Kbp 13 13.69 Mbp
100 7343 4.93 Kbp 1550 4.93 Kbp
1.000x 7343 2.07 Gbp 1550 2.07 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 2 December 2025
fAleTen1.HiC.hap2.20251202.fasta.gz (529.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 64 2.35 Mbp 1 310.79 Mbp
20 173 1.67 Mbp 2 196.55 Mbp
30 321 1.27 Mbp 3 194.80 Mbp
40 517 0.93 Mbp 4 181.64 Mbp
50 775 0.72 Mbp 6 173.46 Mbp
60 1125 0.52 Mbp 7 170.23 Mbp
70 1613 369.10 Kbp 8 146.22 Mbp
80 2326 237.65 Kbp 10 134.12 Mbp
90 3562 120.79 Kbp 16 3.66 Mbp
100 7449 7.17 Kbp 1499 7.17 Kbp
1.000x 7449 2.13 Gbp 1499 2.13 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 1 December 2025
fAleTen1.MT.20251201.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fAleTen1.yml (view)
species: Alepocephalus tenebrosus
specimem: fAleTen1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Alepocephalus_tenebrosus/fAleTen1/assembly_vgp_HiC_2.0/fAleTen1.HiC.hap1.20251202.fasta.gz
hap2: s3://genomeark/species/Alepocephalus_tenebrosus/fAleTen1/assembly_vgp_HiC_2.0/fAleTen1.HiC.hap2.20251202.fasta.gz
pretext_hap1: s3://genomeark/species/Alepocephalus_tenebrosus/fAleTen1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fAleTen1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Alepocephalus_tenebrosus/fAleTen1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fAleTen1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Alepocephalus_tenebrosus/fAleTen1/assembly_vgp_HiC_2.0/evaluation/merqury/fAleTen1_png/
pacbio_read_dir: s3://genomeark/species/Alepocephalus_tenebrosus/fAleTen1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Alepocephalus_tenebrosus/fAleTen1/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 fAleTen1 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.