Dermatemys mawii

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) rDerMaw1 126.59 Gbp N/A 59.5 GiB
PacBio HiFi (.bam) rDerMaw1 129.18 Gbp N/A 419.3 GiB
Arima rDerMaw1 155.52 Gbp N/A 85.7 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
rDerMaw1 PacBio HiFi (.fq) 126.59 Gbp N/A 59.5 GiB
PacBio HiFi (.bam) 129.18 Gbp N/A 419.3 GiB
Arima 155.52 Gbp N/A 85.7 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 25 August 2025
rDerMaw1.HiC.hap1.20250825.fasta.gz (504.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 143.08 Mbp 1 302.73 Mbp
20 3 133.22 Mbp 2 227.12 Mbp
30 5 93.34 Mbp 3 172.35 Mbp
40 8 70.57 Mbp 4 116.33 Mbp
50 11 60.17 Mbp 6 112.99 Mbp
60 14 45.23 Mbp 8 93.52 Mbp
70 20 28.86 Mbp 10 75.31 Mbp
80 29 17.79 Mbp 13 52.71 Mbp
90 47 5.10 Mbp 20 18.97 Mbp
100 322 16.46 Kbp 206 16.46 Kbp
1.000x 322 1.97 Gbp 206 1.97 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 25 August 2025
rDerMaw1.HiC.hap2.20250825.fasta.gz (512.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 112.06 Mbp 1 303.28 Mbp
20 4 109.64 Mbp 2 227.65 Mbp
30 6 102.12 Mbp 3 172.61 Mbp
40 8 88.01 Mbp 4 115.28 Mbp
50 10 78.14 Mbp 6 110.99 Mbp
60 13 65.28 Mbp 8 92.73 Mbp
70 17 34.29 Mbp 10 74.26 Mbp
80 25 19.04 Mbp 14 34.10 Mbp
90 46 4.63 Mbp 23 17.94 Mbp
100 624 16.46 Kbp 247 16.46 Kbp
1.000x 624 1.97 Gbp 247 1.97 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 25 August 2025
rDerMaw1.MT.20250825.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/rDerMaw1.yml (view)
species: Dermatemys mawii
specimem: rDerMaw1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Dermatemys_mawii/rDerMaw1/assembly_vgp_HiC_2.0/rDerMaw1.HiC.hap1.20250825.fasta.gz
hap2: s3://genomeark/species/Dermatemys_mawii/rDerMaw1/assembly_vgp_HiC_2.0/rDerMaw1.HiC.hap2.20250825.fasta.gz
pretext_hap1: s3://genomeark/species/Dermatemys_mawii/rDerMaw1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/rDerMaw1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Dermatemys_mawii/rDerMaw1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/rDerMaw1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Dermatemys_mawii/rDerMaw1/assembly_vgp_HiC_2.0/evaluation/merqury/rDerMaw1_png/
pacbio_read_dir: s3://genomeark/species/Dermatemys_mawii/rDerMaw1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Dermatemys_mawii/rDerMaw1/genomic_data/arima/
pipeline:
  - hifiasm (v0.25.0+galaxy0)
  - yahs (v1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.1)
  - VGP1 genomic profiling workflow (v0.3)
  - VGP4 HiFi HiC assembly workflow (v0.3.8)
  - VGP8 HiC scaffolding workflow (v2.0)
  - FCS-GX decontamination workflow (ncbi_fcs_adaptor v0.5.0+galaxy0)
  - Pre-curation worklfow (v1.0beta6)
notes: This was a Hifiasm-HiC assembly of rDerMaw1 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.