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_curated from 26 March 2026
fAleTen1.hap1.cur.20260326.fasta.gz (582.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 63 2.42 Mbp 2 192.41 Mbp
20 172 1.66 Mbp 3 183.04 Mbp
30 317 1.29 Mbp 4 182.82 Mbp
40 508 0.96 Mbp 5 176.70 Mbp
50 758 0.73 Mbp 6 176.68 Mbp
60 1095 0.53 Mbp 7 174.80 Mbp
70 1572 367.45 Kbp 9 139.83 Mbp
80 2280 236.03 Kbp 10 132.85 Mbp
90 3526 118.13 Kbp 12 60.10 Mbp
100 7465 10.00 Kbp 1501 10.00 Kbp
1.000x 7465 2.10 Gbp 1501 2.10 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 26 March 2026
fAleTen1.hap2.cur.20260326.fasta.gz (578.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 62 2.48 Mbp 2 191.48 Mbp
20 166 1.66 Mbp 3 181.92 Mbp
30 312 1.26 Mbp 4 179.70 Mbp
40 505 0.93 Mbp 5 176.20 Mbp
50 761 0.71 Mbp 6 172.64 Mbp
60 1100 0.53 Mbp 7 170.34 Mbp
70 1563 383.60 Kbp 9 138.20 Mbp
80 2254 237.96 Kbp 10 131.95 Mbp
90 3473 121.77 Kbp 13 54.34 Mbp
100 7273 10.02 Kbp 1461 10.02 Kbp
1.000x 7273 2.10 Gbp 1461 2.10 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.