Paroedura picta

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) rParPic3 147.40 Gbp N/A 67.9 GiB
PacBio HiFi (.bam) rParPic3 148.18 Gbp N/A 488.5 GiB
Arima rParPic1 180.47 Gbp N/A 98.3 GiB
rParPic3 229.33 Gbp N/A 120.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 24 June 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rParPic1 Arima 180.47 Gbp N/A 98.3 GiB
rParPic3 PacBio HiFi (.fq) 147.40 Gbp N/A 67.9 GiB
PacBio HiFi (.bam) 148.18 Gbp N/A 488.5 GiB
Arima 229.33 Gbp N/A 120.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 24 June 2025.
Assemblies
Individual 3 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 6 October 2025
rParPic3.HiC.hap1.20251006.fasta.gz (437.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 201.15 Mbp 1 354.25 Mbp
20 2 172.05 Mbp 1 354.25 Mbp
30 3 135.89 Mbp 2 182.02 Mbp
40 5 120.76 Mbp 3 176.46 Mbp
50 6 112.25 Mbp 5 126.42 Mbp
60 8 88.12 Mbp 6 119.28 Mbp
70 10 58.40 Mbp 7 104.11 Mbp
80 14 41.98 Mbp 9 80.68 Mbp
90 19 21.90 Mbp 12 53.69 Mbp
100 75 25.91 Kbp 49 25.91 Kbp
1.000x 75 1.69 Gbp 49 1.69 Gbp
NG based on genome size .
Individual 3 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 6 October 2025
rParPic3.HiC.hap2.20251006.fasta.gz (439.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 199.15 Mbp 1 208.80 Mbp
20 2 173.86 Mbp 2 183.86 Mbp
30 4 125.34 Mbp 3 177.43 Mbp
40 5 118.11 Mbp 4 144.08 Mbp
50 6 105.85 Mbp 5 134.18 Mbp
60 8 90.78 Mbp 7 123.81 Mbp
70 10 82.14 Mbp 8 118.67 Mbp
80 13 53.68 Mbp 10 89.02 Mbp
90 18 22.59 Mbp 12 66.53 Mbp
100 64 26.05 Kbp 43 26.05 Kbp
1.000x 64 1.69 Gbp 43 1.69 Gbp
NG based on genome size .
Individual 3 Mitochondrial Assembly
Version assembly_MT_rockefeller from 6 October 2025
rParPic3.MT.20251006.fasta.gz (5.5 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/rParPic3.yml (view)
species: Paroedura picta
specimem: rParPic3
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Paroedura_picta/rParPic3/assembly_vgp_HiC_2.0/rParPic3.HiC.hap1.20251006.fasta.gz
hap2: s3://genomeark/species/Paroedura_picta/rParPic3/assembly_vgp_HiC_2.0/rParPic3.HiC.hap2.20251006.fasta.gz
pretext_hap1: s3://genomeark/species/Paroedura_picta/rParPic3/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/rParPic3_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Paroedura_picta/rParPic3/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/rParPic3_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Paroedura_picta/rParPic3/assembly_vgp_HiC_2.0/evaluation/merqury/rParPic3_png/
pacbio_read_dir: s3://genomeark/species/Paroedura_picta/rParPic3/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Paroedura_picta/rParPic3/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 unpublished using FCS (0.5.5+galaxy0) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of rParPic3 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.