Rhinophrynus dorsalis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) aRhiDor1 3131.40 Gbp N/A 5.3 TiB
PacBio HiFi (.fq) aRhiDor1 136.10 Gbp N/A 98.6 GiB
PacBio HiFi (.bam) aRhiDor1 427.27 Gbp N/A 1.4 TiB
Arima aRhiDor1 397.11 Gbp N/A 205.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 9 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aRhiDor1 PacBio HiFi (subreads) 3131.40 Gbp N/A 5.3 TiB
PacBio HiFi (.fq) 136.10 Gbp N/A 98.6 GiB
PacBio HiFi (.bam) 427.27 Gbp N/A 1.4 TiB
Arima 397.11 Gbp N/A 205.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 9 June 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 6 March 2024
aRhiDor1.hap1.cur.20240306.fasta.gz (1.3 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 9 40.45 Mbp 1 0.70 Gbp
20 22 30.99 Mbp 2 0.64 Gbp
30 39 24.48 Mbp 3 0.57 Gbp
40 62 18.00 Mbp 3 0.57 Gbp
50 92 12.99 Mbp 4 0.57 Gbp
60 137 8.71 Mbp 5 0.51 Gbp
70 207 5.26 Mbp 6 498.19 Mbp
80 335 2.66 Mbp 7 404.87 Mbp
90 630 1.01 Mbp 9 200.99 Mbp
100 2495 14.63 Kbp 463 14.63 Kbp
1.000x 2495 4.75 Gbp 463 4.75 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 7 March 2024
aRhiDor1.hap2.cur.20240307.fasta.gz (1.2 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 8 42.50 Mbp 1 0.69 Gbp
20 20 30.34 Mbp 2 0.62 Gbp
30 37 22.66 Mbp 3 0.54 Gbp
40 61 17.07 Mbp 3 0.54 Gbp
50 92 12.72 Mbp 4 0.53 Gbp
60 136 8.46 Mbp 5 499.95 Mbp
70 201 5.48 Mbp 6 468.90 Mbp
80 311 3.05 Mbp 7 387.09 Mbp
90 561 1.04 Mbp 9 193.08 Mbp
100 2665 6.09 Kbp 656 6.09 Kbp
1.000x 2665 4.53 Gbp 656 4.54 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 16 October 2023
aRhiDor1.MT.20231016.fasta.gz (5.5 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/aRhiDor1_hap1.yml (view)
species: Rhinophrynus dorsalis
specimen: aRhiDor1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Rhinophrynus_dorsalis/aRhiDor1/assembly_vgp_HiC_2.0/aRhiDor1.HiC.hap1.20231016.fasta.gz
hap2: s3://genomeark/species/Rhinophrynus_dorsalis/aRhiDor1/assembly_vgp_HiC_2.0/aRhiDor1.HiC.hap2.20231016.fasta.gz
pretext_hap1: s3://genomeark/species/Rhinophrynus_dorsalis/aRhiDor1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/aRhiDor1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Rhinophrynus_dorsalis/aRhiDor1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/aRhiDor1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Rhinophrynus_dorsalis/aRhiDor1/assembly_vgp_HiC_2.0/evaluation/merqury/aRhiDor1_png/
pacbio_read_dir: s3://genomeark/species/Rhinophrynus_dorsalis/aRhiDor1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Rhinophrynus_dorsalis/aRhiDor1/genomic_data/arima/
mito: s3://genomeark/species/Rhinophrynus_dorsalis/aRhiDor1/assembly_MT_rockefeller/aRhiDor1.MT.20231016.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - purge_dups
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of aRhiDor1, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Arima library prep. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. 
assembly_vgp_HiC_2.0/aRhiDor1_hap2.yml (view)
species: Rhinophrynus dorsalis
specimen: aRhiDor1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Rhinophrynus_dorsalis/aRhiDor1/assembly_vgp_HiC_2.0/aRhiDor1.HiC.hap1.20231016.fasta.gz
hap2: s3://genomeark/species/Rhinophrynus_dorsalis/aRhiDor1/assembly_vgp_HiC_2.0/aRhiDor1.HiC.hap2.20231016.fasta.gz
pretext_hap1: s3://genomeark/species/Rhinophrynus_dorsalis/aRhiDor1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/aRhiDor1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Rhinophrynus_dorsalis/aRhiDor1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/aRhiDor1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Rhinophrynus_dorsalis/aRhiDor1/assembly_vgp_HiC_2.0/evaluation/merqury/aRhiDor1_png/
pacbio_read_dir: s3://genomeark/species/Rhinophrynus_dorsalis/aRhiDor1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Rhinophrynus_dorsalis/aRhiDor1/genomic_data/arima/
mito: s3://genomeark/species/Rhinophrynus_dorsalis/aRhiDor1/assembly_MT_rockefeller/aRhiDor1.MT.20231016.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - purge_dups
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of aRhiDor1, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Arima library prep. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. 
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.