Datnioides polota

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fDatPol1 31.95 Gbp N/A 15.5 GiB
PacBio HiFi (.bam) fDatPol1 31.77 Gbp N/A 125.6 GiB
Arima fDatPol1 139.70 Gbp N/A 74.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 October 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fDatPol1 PacBio HiFi (.fq) 31.95 Gbp N/A 15.5 GiB
PacBio HiFi (.bam) 31.77 Gbp N/A 125.6 GiB
Arima 139.70 Gbp N/A 74.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 October 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 17 October 2025
fDatPol1.HiC.hap1.20251017.fasta.gz (152.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 22.10 Mbp 2 29.61 Mbp
20 6 20.54 Mbp 4 28.17 Mbp
30 8 19.99 Mbp 6 27.81 Mbp
40 11 18.63 Mbp 9 26.45 Mbp
50 15 16.02 Mbp 11 25.71 Mbp
60 18 15.26 Mbp 13 24.80 Mbp
70 23 12.70 Mbp 15 24.20 Mbp
80 32 4.27 Mbp 18 22.82 Mbp
90 50 2.38 Mbp 21 20.55 Mbp
100 187 10.47 Kbp 73 10.47 Kbp
1.000x 187 0.58 Gbp 73 0.58 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 17 October 2025
fDatPol1.HiC.hap2.20251017.fasta.gz (153.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 25.50 Mbp 2 29.92 Mbp
20 5 24.50 Mbp 4 28.01 Mbp
30 8 20.69 Mbp 6 27.15 Mbp
40 10 19.46 Mbp 8 26.56 Mbp
50 14 16.89 Mbp 10 25.81 Mbp
60 17 16.25 Mbp 13 24.71 Mbp
70 22 10.10 Mbp 15 24.28 Mbp
80 30 4.63 Mbp 18 22.29 Mbp
90 50 2.20 Mbp 20 20.21 Mbp
100 157 10.47 Kbp 53 10.47 Kbp
1.000x 157 0.58 Gbp 53 0.58 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 17 October 2025
fDatPol1.MT.20251017.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fDatPol1.yml (view)
species: Datnioides polota
specimem: fDatPol1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Datnioides_polota/fDatPol1/assembly_vgp_HiC_2.0/fDatPol1.HiC.hap1.20251017.fasta.gz
hap2: s3://genomeark/species/Datnioides_polota/fDatPol1/assembly_vgp_HiC_2.0/fDatPol1.HiC.hap2.20251017.fasta.gz
pretext_hap1: s3://genomeark/species/Datnioides_polota/fDatPol1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fDatPol1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Datnioides_polota/fDatPol1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fDatPol1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Datnioides_polota/fDatPol1/assembly_vgp_HiC_2.0/evaluation/merqury/fDatPol1_png/
pacbio_read_dir: s3://genomeark/species/Datnioides_polota/fDatPol1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Datnioides_polota/fDatPol1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.1)
  - VGP1 genomic profiling workflow (v0.2)
  - VGP4 HiFi HiC assembly workflow (v0.3.6)
  - VGP8 HiC scaffolding workflow (v1.8)
  - VGP9 decontamination workflow (v0.6) using Kraken2 database 2022-09-04T165121Z_standard_prebuilt_pluspf_2022-06-07 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of fDatPol1 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. The mitochondrial assembly suggests the HiFi data is from species Datnioides polota.
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.