Cardinalis cardinalis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bCarCad1 49.44 Gbp N/A 22.6 GiB
PacBio HiFi (.bam) bCarCad1 50.49 Gbp N/A 162.1 GiB
Arima bCarCad1 125.16 Gbp N/A 66.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 October 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bCarCad1 PacBio HiFi (.fq) 49.44 Gbp N/A 22.6 GiB
PacBio HiFi (.bam) 50.49 Gbp N/A 162.1 GiB
Arima 125.16 Gbp N/A 66.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 October 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 17 October 2025
bCarCad1.HiC.hap1.20251017.fasta.gz (279.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 51.86 Mbp 1 153.54 Mbp
20 6 28.61 Mbp 2 120.58 Mbp
30 10 23.79 Mbp 3 117.95 Mbp
40 15 19.41 Mbp 4 76.34 Mbp
50 22 14.16 Mbp 6 64.32 Mbp
60 32 9.71 Mbp 8 36.04 Mbp
70 46 6.89 Mbp 12 24.37 Mbp
80 67 3.93 Mbp 17 19.67 Mbp
90 113 1.29 Mbp 26 7.78 Mbp
100 831 5.45 Kbp 584 5.45 Kbp
1.000x 831 1.12 Gbp 584 1.12 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 17 October 2025
bCarCad1.HiC.hap2.20251017.fasta.gz (314.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 33.57 Mbp 1 154.30 Mbp
20 8 26.41 Mbp 2 120.41 Mbp
30 14 19.20 Mbp 4 78.58 Mbp
40 22 15.12 Mbp 5 74.39 Mbp
50 32 11.99 Mbp 8 43.37 Mbp
60 46 7.30 Mbp 11 26.05 Mbp
70 66 5.49 Mbp 18 19.20 Mbp
80 101 2.84 Mbp 26 12.04 Mbp
90 192 0.64 Mbp 48 2.07 Mbp
100 1402 12.09 Kbp 1065 12.09 Kbp
1.000x 1402 1.33 Gbp 1065 1.33 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 17 October 2025
bCarCad1.MT.20251017.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bCarCad1.yml (view)
species: Cardinalis cardinalis
specimem: bCarCad1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Cardinalis_cardinalis/bCarCad1/assembly_vgp_HiC_2.0/bCarCad1.HiC.hap1.20251017.fasta.gz
hap2: s3://genomeark/species/Cardinalis_cardinalis/bCarCad1/assembly_vgp_HiC_2.0/bCarCad1.HiC.hap2.20251017.fasta.gz
pretext_hap1: s3://genomeark/species/Cardinalis_cardinalis/bCarCad1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bCarCad1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Cardinalis_cardinalis/bCarCad1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bCarCad1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Cardinalis_cardinalis/bCarCad1/assembly_vgp_HiC_2.0/evaluation/merqury/bCarCad1_png/
pacbio_read_dir: s3://genomeark/species/Cardinalis_cardinalis/bCarCad1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Cardinalis_cardinalis/bCarCad1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.4)
  - VGP8 HiC scaffolding workflow (v3.1) with default mapq=10
  - VGP9 decontamination workflow (v1.1) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of bCarCad1 resulting in two haplotype assemblies. HiC data were generated using the Arima library prep kit, and require trimming the first 5 bp off from the 5' end of both read files. The restriction enzymes used were the Arima v2 kit, so the cutting sites are GATC, GANTC, CTNAG, TTAA.
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.