Platysternon megacephalum

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) rPlaMeg1 162.82 Gbp N/A 80.1 GiB
PacBio HiFi (.bam) rPlaMeg1 166.51 Gbp N/A 547.0 GiB
Arima rPlaMeg1 125.59 Gbp N/A 69.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 30 November 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rPlaMeg1 PacBio HiFi (.fq) 162.82 Gbp N/A 80.1 GiB
PacBio HiFi (.bam) 166.51 Gbp N/A 547.0 GiB
Arima 125.59 Gbp N/A 69.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 30 November 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 12 December 2025
rPlaMeg1.HiC.hap1.20251212.fasta.gz (591.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 160.05 Mbp 1 352.42 Mbp
20 3 134.88 Mbp 2 297.29 Mbp
30 5 105.05 Mbp 3 206.24 Mbp
40 7 84.99 Mbp 4 183.37 Mbp
50 10 76.76 Mbp 5 148.96 Mbp
60 13 67.53 Mbp 6 144.82 Mbp
70 17 42.35 Mbp 8 107.13 Mbp
80 23 30.17 Mbp 11 46.27 Mbp
90 31 20.16 Mbp 17 27.26 Mbp
100 303 15.00 Kbp 133 15.00 Kbp
1.000x 303 2.19 Gbp 133 2.19 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 12 December 2025
rPlaMeg1.HiC.hap2.20251212.fasta.gz (597.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 262.51 Mbp 1 477.23 Mbp
20 2 184.53 Mbp 1 477.23 Mbp
30 4 144.07 Mbp 2 350.93 Mbp
40 6 126.74 Mbp 3 149.13 Mbp
50 8 107.26 Mbp 4 143.37 Mbp
60 10 85.57 Mbp 6 130.04 Mbp
70 13 45.14 Mbp 8 107.26 Mbp
80 18 42.52 Mbp 11 47.77 Mbp
90 26 18.17 Mbp 15 43.36 Mbp
100 232 14.30 Kbp 91 14.30 Kbp
1.000x 232 2.22 Gbp 91 2.22 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 12 December 2025
rPlaMeg1.MT.20251212.fasta.gz (7.7 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/rPlaMeg1.yml (view)
species: Platysternon megacephalum
specimem: rPlaMeg1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Platysternon_megacephalum/rPlaMeg1/assembly_vgp_HiC_2.0/rPlaMeg1.HiC.hap1.20251212.fasta.gz
hap2: s3://genomeark/species/Platysternon_megacephalum/rPlaMeg1/assembly_vgp_HiC_2.0/rPlaMeg1.HiC.hap2.20251212.fasta.gz
pretext_hap1: s3://genomeark/species/Platysternon_megacephalum/rPlaMeg1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/rPlaMeg1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Platysternon_megacephalum/rPlaMeg1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/rPlaMeg1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Platysternon_megacephalum/rPlaMeg1/assembly_vgp_HiC_2.0/evaluation/merqury/rPlaMeg1_png/
pacbio_read_dir: s3://genomeark/species/Platysternon_megacephalum/rPlaMeg1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Platysternon_megacephalum/rPlaMeg1/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 rPlaMeg1 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.