Pelodiscus sinensis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) rPelSin1 144.75 Gbp N/A 73.6 GiB
PacBio HiFi (.bam) rPelSin1 147.62 Gbp N/A 486.1 GiB
Arima rPelSin1 494.70 Gbp N/A 265.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 10 March 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rPelSin1 PacBio HiFi (.fq) 144.75 Gbp N/A 73.6 GiB
PacBio HiFi (.bam) 147.62 Gbp N/A 486.1 GiB
Arima 494.70 Gbp N/A 265.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 10 March 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 7 July 2025
rPelSin1.hap1.decontam.20250707.fasta.gz (607.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 133.95 Mbp 1 354.69 Mbp
20 4 124.65 Mbp 2 259.76 Mbp
30 5 114.52 Mbp 3 198.03 Mbp
40 8 74.24 Mbp 4 133.95 Mbp
50 11 69.20 Mbp 6 128.06 Mbp
60 16 43.96 Mbp 9 69.20 Mbp
70 22 32.57 Mbp 12 54.33 Mbp
80 31 11.73 Mbp 17 42.11 Mbp
90 69 2.97 Mbp 24 22.21 Mbp
100 798 16.60 Kbp 423 16.60 Kbp
1.000x 798 2.26 Gbp 423 2.26 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 7 July 2025
rPelSin1.hap2.decontam.20250707.fasta.gz (568.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 171.65 Mbp 1 349.87 Mbp
20 3 126.19 Mbp 2 250.90 Mbp
30 5 79.23 Mbp 3 193.60 Mbp
40 8 73.46 Mbp 4 129.17 Mbp
50 10 71.46 Mbp 6 125.23 Mbp
60 14 49.93 Mbp 8 71.46 Mbp
70 20 33.60 Mbp 11 47.51 Mbp
80 28 17.06 Mbp 16 37.24 Mbp
90 68 2.49 Mbp 25 14.96 Mbp
100 704 15.84 Kbp 380 15.84 Kbp
1.000x 704 2.11 Gbp 380 2.11 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 7 July 2025
rPelSin1.MT.20250707.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/rPelSin1.yml (view)
species: Pelodiscus sinensis
specimem: rPelSin1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: false
hap1: s3://genomeark/species/Pelodiscus_sinensis/rPelSin1/assembly_vgp_HiC_2.0/rPelSin1.HiC.hap1.20250707.fasta.gz
hap2: s3://genomeark/species/Pelodiscus_sinensis/rPelSin1/assembly_vgp_HiC_2.0/rPelSin1.HiC.hap2.20250707.fasta.gz
pretext_hap1: s3://genomeark/species/Pelodiscus_sinensis/rPelSin1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/rPelSin1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Pelodiscus_sinensis/rPelSin1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/rPelSin1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Pelodiscus_sinensis/rPelSin1/assembly_vgp_HiC_2.0/evaluation/merqury/rPelSin1_png/
pacbio_read_dir: s3://genomeark/species/Pelodiscus_sinensis/rPelSin1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Pelodiscus_sinensis/rPelSin1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.1)
  - VGP1 genomic profiling workflow (v0.3)
  - VGP4 HiFi HiC assembly workflow (v0.3.8)
  - VGP8 HiC scaffolding workflow (v2.0)
  - VGP9 decontamination workflow (v0.7) with Kranken2 database PlusPF 2022
notes: This was a Hifiasm-HiC assembly of rPelSin1 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. Decide not to curate the genome due to sparse HiC signals in PretextMap. Only new HiC data was used in assembly.
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.