Cyclura pinguis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) rCycPin1 1404.18 Gbp N/A 2.4 TiB
PacBio HiFi (.fq) rCycPin1 228.67 Gbp N/A 134.3 GiB
PacBio HiFi (.bam) rCycPin1 181.43 Gbp N/A 637.4 GiB
Dovetail Genomics rCycPin1 428.42 Gbp N/A 216.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 21 February 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rCycPin1 PacBio HiFi (subreads) 1404.18 Gbp N/A 2.4 TiB
PacBio HiFi (.fq) 228.67 Gbp N/A 134.3 GiB
PacBio HiFi (.bam) 181.43 Gbp N/A 637.4 GiB
Dovetail Genomics 428.42 Gbp N/A 216.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 21 February 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 21 March 2023
rCycPin1.HiC.hap1.20230321.fasta.gz (567.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 0 209.56 Mbp 0 392.46 Mbp
20 1 189.69 Mbp 0 392.46 Mbp
30 2 182.90 Mbp 1 347.47 Mbp
40 4 149.83 Mbp 2 291.69 Mbp
50 5 123.36 Mbp 2 291.69 Mbp
60 7 105.67 Mbp 3 267.94 Mbp
70 9 103.81 Mbp 4 218.38 Mbp
80 11 42.78 Mbp 5 142.80 Mbp
90 17 22.32 Mbp 8 33.43 Mbp
100 54 14.01 Kbp 34 14.01 Kbp
1.000x 55 1.94 Gbp 35 1.96 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 2 May 2023
rCycPin1.HiC.hap2.20230502.fasta.gz (538.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 183.25 Mbp 1 392.53 Mbp
20 3 162.99 Mbp 2 357.52 Mbp
30 4 155.16 Mbp 2 357.52 Mbp
40 5 133.65 Mbp 3 291.72 Mbp
50 7 112.81 Mbp 3 291.72 Mbp
60 9 105.10 Mbp 4 268.10 Mbp
70 11 76.13 Mbp 5 218.51 Mbp
80 14 45.38 Mbp 6 143.87 Mbp
90 21 19.45 Mbp 10 33.44 Mbp
100 58 32.99 Kbp 30 32.99 Kbp
1.000x 58 1.98 Gbp 30 1.98 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 10 February 2023
rCycPin1.MT.20230210.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/rCycPin1.yml (view)
species: Cyclura pinguis
specimen: rCycPin1
projects: 
  - vgp
data_location: S3
release_to: S3
hap1: s3://genomeark/species/Cyclura_pinguis/rCycPin1/assembly_vgp_HiC_2.0/rCycPin1.HiC.hap1.20230321.fasta.gz
hap2: s3://genomeark/species/Cyclura_pinguis/rCycPin1/assembly_vgp_HiC_2.0/rCycPin1.HiC.hap2.20230321.fasta.gz
pretext_hap1: s3://genomeark/species/Cyclura_pinguis/rCycPin1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/rCycPin1_hap1__s1_heatmap.pretext
pretext_hap2: s3://genomeark/species/Cyclura_pinguis/rCycPin1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rCycPin1_hap2__s1_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Cyclura_pinguis/rCycPin1/assembly_vgp_HiC_2.0/evaluation/merqury/rCycPin1_png/
mito: s3://genomeark/species/Cyclura_pinguis/rCycPin1/assembly_MT_rockefeller/rCycPin1.MT.20230210.fasta.gz
pacbio_read_dir: s3://genomeark/species/Cyclura_pinguis/rCycPin1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Cyclura_pinguis/rCycPin1/genomic_data/dovetail/
bionano_cmap_dir: s3://genomeark/species/Cyclura_pinguis/rCycPin1/genomic_data/bionano/
pipeline:
  - hifiasm (0.16.1+galaxy4)
  - solve (3.7)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of rCycPin1, resulting in two complete haplotypes. This individual had bionano data. HiC scaffolding was not performed, as when it was attempted, it resulted in no new joins. So these assemblies have only Bionano scaffolding. The kmer spectra indicates a homogametic specimen. 
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.