Potamotrygon marinae

gold dust stingray

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  short_name: sPotMar
  name: Potamotrygon marinae
  taxon_id: null
  common_name: gold dust stingray
  order:
    name: Myliobatiformes
  family:
    name: Potamotrygonidae
  individuals:
    - short_name: sPotMar1
      sex: male
      provider: Yann Guiguen, Julien Bobe, Gavin Naylor
  genome_size: 4500000000
  genome_size_method:
  project: [ vgp ]
No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio CLR sPotMar1 312.43 Gbp 69.43x 552.9 GiB
PacBio HiFi (.fq) sPotMar1 164.25 Gbp 36.50x 84.7 GiB
PacBio HiFi (.bam) sPotMar1 167.22 Gbp 37.16x 667.5 GiB
Arima sPotMar1 248.93 Gbp 55.32x 163.8 GiB
Illumina sPotMar1 344.26 Gbp 76.50x 162.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 4.50 Gbp.
Last upload on 5 March 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
sPotMar1 PacBio CLR 312.43 Gbp 69.43x 552.9 GiB
PacBio HiFi (.fq) 164.25 Gbp 36.50x 84.7 GiB
PacBio HiFi (.bam) 167.22 Gbp 37.16x 667.5 GiB
Arima 248.93 Gbp 55.32x 163.8 GiB
Illumina 344.26 Gbp 76.50x 162.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 4.50 Gbp.
Last upload on 5 March 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 25 March 2024
sPotMar1.HiC.hap1.20240325.fasta.gz (1.3 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 8 50.18 Mbp 2 237.35 Mbp
20 20 34.60 Mbp 4 209.51 Mbp
30 35 26.09 Mbp 6 203.98 Mbp
40 54 20.28 Mbp 9 197.52 Mbp
50 81 14.70 Mbp 11 186.85 Mbp
60 119 10.48 Mbp 14 108.44 Mbp
70 171 7.05 Mbp 19 86.99 Mbp
80 250 4.32 Mbp 25 59.97 Mbp
90 390 2.33 Mbp 34 20.01 Mbp
100 687 0.94 Mbp 145 1.79 Mbp
1.079x 2055 4.86 Gbp 1237 4.86 Gbp
NG based on genome size 4.50 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 25 March 2024
sPotMar1.HiC.hap2.20240325.fasta.gz (1.2 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 9 42.24 Mbp 2 235.42 Mbp
20 21 30.70 Mbp 4 204.62 Mbp
30 38 22.10 Mbp 6 202.06 Mbp
40 61 16.51 Mbp 9 193.50 Mbp
50 93 12.06 Mbp 11 137.10 Mbp
60 139 8.16 Mbp 15 103.92 Mbp
70 207 5.16 Mbp 20 82.86 Mbp
80 335 2.45 Mbp 27 49.43 Mbp
90 627 0.95 Mbp 83 2.75 Mbp
100 0 0
0.985x 1888 4.43 Gbp 968 4.43 Gbp
NG based on genome size 4.50 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/sPotMar1.yml (view)
species: Potamotrygon marinae
specimen: sPotMar1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Potamotrygon_marinae/sPotMar1/assembly_vgp_HiC_2.0/sPotMar1.HiC.hap1.20240325.fasta.gz
hap2: s3://genomeark/species/Potamotrygon_marinae/sPotMar1/assembly_vgp_HiC_2.0/sPotMar1.HiC.hap2.20240325.fasta.gz
pretext_hap1: s3://genomeark/species/Potamotrygon_marinae/sPotMar1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/sPotMar1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Potamotrygon_marinae/sPotMar1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/sPotMar1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Potamotrygon_marinae/sPotMar1/assembly_vgp_HiC_2.0/evaluation/merqury/sPotMar1_png/
pacbio_read_dir: s3://genomeark/species/Potamotrygon_marinae/sPotMar1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Potamotrygon_marinae/sPotMar1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of sPotMar1, resulting in two complete haplotypes. There was no Bionano data, and the scaffolding consisted of YaHS. The HiC prep kit used was Arima, so the HiC reads require trimming 5 bp off the 5' end. The assembly was performed on the Rockefeller University VGL instance. 
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.