Bradypodion pumilum

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) rBraPum1 121.53 Gbp N/A 86.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 30 August 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rBraPum1 PacBio HiFi (.fq) 121.53 Gbp N/A 86.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 30 August 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 26 September 2024
rBraPum1.hap1.cur.20240926.fasta.gz (704.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 115.13 Mbp 1 0.52 Gbp
20 5 73.42 Mbp 1 0.52 Gbp
30 9 67.95 Mbp 2 483.74 Mbp
40 13 51.26 Mbp 2 483.74 Mbp
50 18 44.37 Mbp 3 387.40 Mbp
60 24 32.73 Mbp 4 345.61 Mbp
70 32 27.93 Mbp 4 345.61 Mbp
80 42 20.50 Mbp 5 266.41 Mbp
90 59 10.47 Mbp 8 42.92 Mbp
100 182 23.05 Kbp 73 23.05 Kbp
1.000x 182 2.47 Gbp 73 2.47 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 26 September 2024
rBraPum1.hap2.cur.20240926.fasta.gz (706.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 91.47 Mbp 1 0.52 Gbp
20 6 80.49 Mbp 1 0.52 Gbp
30 9 77.57 Mbp 2 476.61 Mbp
40 12 71.51 Mbp 2 476.61 Mbp
50 16 53.35 Mbp 3 388.71 Mbp
60 22 34.57 Mbp 4 348.68 Mbp
70 30 26.65 Mbp 5 268.34 Mbp
80 41 17.44 Mbp 5 268.34 Mbp
90 61 8.44 Mbp 8 43.63 Mbp
100 202 23.05 Kbp 82 23.05 Kbp
1.000x 202 2.48 Gbp 82 2.48 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/rBraPum1.yml (view)
species: Bradypodion pumilum
specimen: rBraPum1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Bradypodion_pumilum/rBraPum1/assembly_vgp_HiC_2.0/rBraPum1.HiC.hap1.20240820.fasta.gz
hap2: s3://genomeark/species/Bradypodion_pumilum/rBraPum1/assembly_vgp_HiC_2.0/rBraPum1.HiC.hap2.20240820.fasta.gz
pretext_hap1: s3://genomeark/species/Bradypodion_pumilum/rBraPum1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/rBraPum1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Bradypodion_pumilum/rBraPum1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rBraPum1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Bradypodion_pumilum/rBraPum1/assembly_vgp_HiC_2.0/evaluation/merqury/rBraPum1_png/
pacbio_read_type: hifi
pipeline: 
  - hifiasm (0.19.9+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of rBraPum1, resulting in two complete haplotypes. The HiC data was Dovetail OmniC. The original assembly for this individual is on NCBI as GCA_035047305.1 and was assembled as a pseudohaplotype assembly generated by Dovetail. This 20240820 assembly on GenomeArk is a re-assembly, using hifiasm in Hi-C phsaing mode. The Hi-C data is available on NCBI as SRR24988076. We are submitting these assemblies for dual curation as a Phase 1 genome. 
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.