Pantodon buchholzi

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fPanBuc1 52.88 Gbp N/A 24.4 GiB
PacBio HiFi (.bam) fPanBuc1 54.33 Gbp N/A 175.8 GiB
Arima fPanBuc1 68.42 Gbp N/A 36.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 7 July 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fPanBuc1 PacBio HiFi (.fq) 52.88 Gbp N/A 24.4 GiB
PacBio HiFi (.bam) 54.33 Gbp N/A 175.8 GiB
Arima 68.42 Gbp N/A 36.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 7 July 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 14 October 2025
fPanBuc1.HiC.hap1.20251014.fasta.gz (133.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 24.75 Mbp 2 39.60 Mbp
20 4 22.51 Mbp 3 37.63 Mbp
30 7 19.63 Mbp 5 34.15 Mbp
40 10 17.10 Mbp 6 29.91 Mbp
50 13 14.18 Mbp 8 27.32 Mbp
60 17 12.74 Mbp 10 25.14 Mbp
70 23 8.19 Mbp 12 22.92 Mbp
80 31 5.43 Mbp 15 19.33 Mbp
90 42 3.93 Mbp 18 16.02 Mbp
100 104 19.44 Kbp 41 19.44 Kbp
1.000x 104 0.53 Gbp 41 0.53 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 14 October 2025
fPanBuc1.HiC.hap2.20251014.fasta.gz (133.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 22.74 Mbp 1 64.44 Mbp
20 5 17.33 Mbp 3 37.38 Mbp
30 8 16.33 Mbp 4 34.46 Mbp
40 12 13.19 Mbp 6 27.39 Mbp
50 16 11.05 Mbp 8 25.58 Mbp
60 21 9.33 Mbp 10 23.17 Mbp
70 27 7.64 Mbp 12 20.40 Mbp
80 35 5.97 Mbp 15 16.23 Mbp
90 46 3.57 Mbp 19 13.95 Mbp
100 116 34.55 Kbp 41 35.88 Kbp
1.000x 116 0.53 Gbp 41 0.53 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 14 October 2025
fPanBuc1.MT.20251014.fasta.gz (5.1 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fPanBuc1.yml (view)
species: Pantodon buchholzi
specimem: fPanBuc1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Pantodon_buchholzi/fPanBuc1/assembly_vgp_HiC_2.0/fPanBuc1.HiC.hap1.20251014.fasta.gz
hap2: s3://genomeark/species/Pantodon_buchholzi/fPanBuc1/assembly_vgp_HiC_2.0/fPanBuc1.HiC.hap2.20251014.fasta.gz
pretext_hap1: s3://genomeark/species/Pantodon_buchholzi/fPanBuc1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fPanBuc1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Pantodon_buchholzi/fPanBuc1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fPanBuc1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Pantodon_buchholzi/fPanBuc1/assembly_vgp_HiC_2.0/evaluation/merqury/fPanBuc1_png/
pacbio_read_dir: s3://genomeark/species/Pantodon_buchholzi/fPanBuc1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Pantodon_buchholzi/fPanBuc1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.12)
  - VGP8 HiC scaffolding workflow (v2.2) with mapq=10
  - VGP9 decontamination workflow (v1.0) 
  - VGP6 purge dups workflow (v0.10.4)
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of fPanBuc1 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.