Cyanocitta cristata

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bCyaCrs1 998.94 Gbp N/A 1.7 TiB
PacBio HiFi (.fq) bCyaCrs1 45.63 Gbp N/A 37.1 GiB
PacBio HiFi (.bam) bCyaCrs1 45.54 Gbp N/A 160.2 GiB
Arima bCyaCrs1 44.75 Gbp N/A 24.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 7 November 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bCyaCrs1 PacBio HiFi (subreads) 998.94 Gbp N/A 1.7 TiB
PacBio HiFi (.fq) 45.63 Gbp N/A 37.1 GiB
PacBio HiFi (.bam) 45.54 Gbp N/A 160.2 GiB
Arima 44.75 Gbp N/A 24.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 7 November 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 4 November 2024
bCyaCrs1.hap1.cur.20241104.fasta.gz (340.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 26.31 Mbp 1 158.85 Mbp
20 10 20.25 Mbp 2 122.02 Mbp
30 17 15.05 Mbp 3 118.40 Mbp
40 26 11.56 Mbp 5 77.20 Mbp
50 40 6.93 Mbp 6 76.48 Mbp
60 60 5.22 Mbp 8 42.91 Mbp
70 89 3.61 Mbp 12 27.84 Mbp
80 132 2.23 Mbp 17 19.48 Mbp
90 207 1.25 Mbp 27 7.69 Mbp
100 708 7.82 Kbp 315 17.75 Kbp
1.000x 708 1.23 Gbp 315 1.23 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 4 November 2024
bCyaCrs1.hap2.cur.20241104.fasta.gz (321.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 22.01 Mbp 1 158.51 Mbp
20 12 17.16 Mbp 2 121.56 Mbp
30 20 11.86 Mbp 3 118.59 Mbp
40 32 9.13 Mbp 5 76.39 Mbp
50 47 7.08 Mbp 6 65.83 Mbp
60 66 5.12 Mbp 9 33.48 Mbp
70 94 3.61 Mbp 14 21.17 Mbp
80 139 2.08 Mbp 22 10.94 Mbp
90 221 1.04 Mbp 44 2.12 Mbp
100 642 22.33 Kbp 309 22.33 Kbp
1.000x 642 1.20 Gbp 309 1.20 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 22 April 2024
bCyaCrs1.MT.20240422.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bCyaCrs1.yml (view)
species: Cyanocitta cristata
specimen: bCyaCrs1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Cyanocitta_cristata/bCyaCrs1/assembly_vgp_HiC_2.0/bCyaCrs1.HiC.hap1.20240422.fasta.gz
hap2: s3://genomeark/species/Cyanocitta_cristata/bCyaCrs1/assembly_vgp_HiC_2.0/bCyaCrs1.HiC.hap2.20240422.fasta.gz
pretext_hap1: s3://genomeark/species/Cyanocitta_cristata/bCyaCrs1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bCyaCrs1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Cyanocitta_cristata/bCyaCrs1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bCyaCrs1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Cyanocitta_cristata/bCyaCrs1/assembly_vgp_HiC_2.0/evaluation/merqury/bCyaCrs1_png/
pacbio_read_dir: s3://genomeark/species/Cyanocitta_cristata/bCyaCrs1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Cyanocitta_cristata/bCyaCrs1/genomic_data/arima/
mito: s3://genomeark/species/Cyanocitta_cristata/bCyaCrs1/assembly_MT_rockefeller/bCyaCrs1.MT.20240422.fasta.gz
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of bCyaCrs1, resulting in two complete haplotypes. This sample did not have Bionano. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Swift-IDT library prep. The VGL ID for this specimen is bCyaCrs2.
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.