Candoia aspera

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CC BY 4.0 coenobita (iNaturalist)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) rCanAsp1 192.07 Gbp N/A 428.8 GiB
PacBio HiFi (.fq) rCanAsp1 55.02 Gbp N/A 40.5 GiB
PacBio HiFi (.bam) rCanAsp1 55.45 Gbp N/A 191.7 GiB
Arima rCanAsp1 124.93 Gbp N/A 64.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 14 August 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rCanAsp1 PacBio HiFi (subreads) 192.07 Gbp N/A 428.8 GiB
PacBio HiFi (.fq) 55.02 Gbp N/A 40.5 GiB
PacBio HiFi (.bam) 55.45 Gbp N/A 191.7 GiB
Arima 124.93 Gbp N/A 64.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 14 August 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 23 June 2023
rCanAsp1.hap1.decon.20230623.fasta.gz (444.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 111.79 Mbp 1 338.86 Mbp
20 3 98.33 Mbp 1 338.86 Mbp
30 5 80.97 Mbp 2 263.52 Mbp
40 7 58.58 Mbp 3 209.78 Mbp
50 10 49.53 Mbp 3 209.78 Mbp
60 13 40.63 Mbp 4 117.43 Mbp
70 18 25.57 Mbp 6 109.63 Mbp
80 28 11.73 Mbp 7 100.49 Mbp
90 49 4.94 Mbp 9 78.60 Mbp
100 279 12.16 Kbp 180 12.16 Kbp
1.000x 279 1.53 Gbp 180 1.53 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 23 June 2023
rCanAsp1.hap2.cur.20230623.fasta.gz (444.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 165.64 Mbp 1 343.99 Mbp
20 3 97.99 Mbp 1 343.99 Mbp
30 4 97.80 Mbp 2 265.92 Mbp
40 6 66.25 Mbp 3 209.48 Mbp
50 9 55.64 Mbp 3 209.48 Mbp
60 12 48.64 Mbp 4 119.28 Mbp
70 16 31.91 Mbp 6 100.81 Mbp
80 23 12.97 Mbp 7 84.50 Mbp
90 41 4.99 Mbp 11 25.78 Mbp
100 250 1.00 Kbp 149 1.00 Kbp
1.000x 250 1.53 Gbp 149 1.53 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 10 February 2023
rCanAsp1.MT.20230210.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/rCanAsp1_hap2.yml (view)
species: Candoia aspera
specimen: rCanAsp1
projects: 
  - vgp
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Candoia_aspera/rCanAsp1/assembly_vgp_HiC_2.0/rCanAsp1.HiC.hap1.20230202.fasta.gz
hap2: s3://genomeark/species/Candoia_aspera/rCanAsp1/assembly_vgp_HiC_2.0/rCanAsp1.HiC.hap2.20230202.fasta.gz
pretext_hap1: s3://genomeark/species/Candoia_aspera/rCanAsp1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/rCanAsp1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Candoia_aspera/rCanAsp1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rCanAsp1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Candoia_aspera/rCanAsp1/assembly_vgp_HiC_2.0/evaluation/merqury/rCanAsp1_png/
pacbio_read_dir: s3://genomeark/species/Candoia_aspera/rCanAsp1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Candoia_aspera/rCanAsp1/genomic_data/arima/
pipeline:
  - hifiasm (0.16.1+galaxy3)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of rCanAsp1, resulting in two complete haplotypes. This individual did not have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The kmer spectra indicates a homogametic specimen. We are submitting haplotype 2 for curation.
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.