Passerina cyanea

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bPasCya1 43.85 Gbp N/A 21.8 GiB
PacBio HiFi (.bam) bPasCya1 45.88 Gbp N/A 151.0 GiB
Arima bPasCya1 81.90 Gbp N/A 42.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 September 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bPasCya1 PacBio HiFi (.fq) 43.85 Gbp N/A 21.8 GiB
PacBio HiFi (.bam) 45.88 Gbp N/A 151.0 GiB
Arima 81.90 Gbp N/A 42.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 September 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 3 October 2025
bPasCya1.HiC.hap1.20251003.fasta.gz (336.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 40.07 Mbp 1 153.04 Mbp
20 7 32.51 Mbp 2 118.05 Mbp
30 11 25.05 Mbp 4 87.56 Mbp
40 18 17.65 Mbp 5 75.29 Mbp
50 27 13.54 Mbp 7 62.22 Mbp
60 40 8.46 Mbp 11 25.96 Mbp
70 66 3.83 Mbp 17 16.83 Mbp
80 118 1.86 Mbp 30 8.02 Mbp
90 225 0.76 Mbp 77 1.29 Mbp
100 1205 10.34 Kbp 766 10.34 Kbp
1.000x 1205 1.35 Gbp 766 1.35 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 3 October 2025
bPasCya1.HiC.hap2.20251003.fasta.gz (294.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 34.78 Mbp 1 154.48 Mbp
20 7 31.11 Mbp 2 118.79 Mbp
30 11 21.78 Mbp 3 116.49 Mbp
40 17 18.15 Mbp 4 92.26 Mbp
50 23 15.97 Mbp 6 73.79 Mbp
60 33 10.92 Mbp 7 65.46 Mbp
70 45 7.62 Mbp 10 33.97 Mbp
80 66 4.17 Mbp 15 20.97 Mbp
90 110 1.76 Mbp 22 12.63 Mbp
100 521 11.29 Kbp 244 11.29 Kbp
1.000x 521 1.14 Gbp 244 1.14 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 3 October 2025
bPasCya1.MT.20251003.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bPasCya1.yml (view)
species: Passerina cyanea
specimem: bPasCya1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Passerina_cyanea/bPasCya1/assembly_vgp_HiC_2.0/bPasCya1.HiC.hap1.20251003.fasta.gz
hap2: s3://genomeark/species/Passerina_cyanea/bPasCya1/assembly_vgp_HiC_2.0/bPasCya1.HiC.hap2.20251003.fasta.gz
pretext_hap1: s3://genomeark/species/Passerina_cyanea/bPasCya1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bPasCya1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Passerina_cyanea/bPasCya1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bPasCya1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Passerina_cyanea/bPasCya1/assembly_vgp_HiC_2.0/evaluation/merqury/bPasCya1_png/
pacbio_read_dir: s3://genomeark/species/Passerina_cyanea/bPasCya1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Passerina_cyanea/bPasCya1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.12)
  - VGP8 HiC scaffolding workflow (v2.2) with mapq=10
  - VGP9 decontamination workflow unpublished using FCS (0.5.5+galaxy0) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of bPasCya1 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.