Passerina amoena

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bPasAmo1 64.79 Gbp N/A 30.6 GiB
PacBio HiFi (.bam) bPasAmo1 66.31 Gbp N/A 204.6 GiB
Arima bPasAmo1 97.20 Gbp N/A 52.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 July 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bPasAmo1 PacBio HiFi (.fq) 64.79 Gbp N/A 30.6 GiB
PacBio HiFi (.bam) 66.31 Gbp N/A 204.6 GiB
Arima 97.20 Gbp N/A 52.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 July 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 23 September 2025
bPasAmo1.HiC.hap1.20250923.fasta.gz (295.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 35.80 Mbp 1 155.25 Mbp
20 7 24.27 Mbp 2 117.64 Mbp
30 13 18.81 Mbp 3 116.77 Mbp
40 20 15.76 Mbp 4 80.07 Mbp
50 28 11.56 Mbp 6 73.83 Mbp
60 41 7.85 Mbp 8 53.84 Mbp
70 60 4.40 Mbp 11 32.48 Mbp
80 95 2.69 Mbp 15 20.93 Mbp
90 157 1.27 Mbp 22 9.22 Mbp
100 723 21.72 Kbp 388 21.73 Kbp
1.000x 723 1.17 Gbp 388 1.17 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 23 September 2025
bPasAmo1.HiC.hap2.20250923.fasta.gz (320.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 27.22 Mbp 1 156.10 Mbp
20 10 19.51 Mbp 2 118.22 Mbp
30 17 16.81 Mbp 4 74.49 Mbp
40 26 12.63 Mbp 5 73.26 Mbp
50 38 9.76 Mbp 8 37.31 Mbp
60 54 7.21 Mbp 12 22.70 Mbp
70 81 3.73 Mbp 19 16.52 Mbp
80 128 2.07 Mbp 29 8.78 Mbp
90 230 0.77 Mbp 56 2.05 Mbp
100 1002 16.99 Kbp 579 16.99 Kbp
1.000x 1002 1.31 Gbp 579 1.31 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 23 September 2025
bPasAmo1.MT.20250923.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bPasAmo1.yml (view)
species: Passerina amoena
specimem: bPasAmo1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Passerina_amoena/bPasAmo1/assembly_vgp_HiC_2.0/bPasAmo1.HiC.hap1.20250923.fasta.gz
hap2: s3://genomeark/species/Passerina_amoena/bPasAmo1/assembly_vgp_HiC_2.0/bPasAmo1.HiC.hap2.20250923.fasta.gz
pretext_hap1: s3://genomeark/species/Passerina_amoena/bPasAmo1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bPasAmo1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Passerina_amoena/bPasAmo1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bPasAmo1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Passerina_amoena/bPasAmo1/assembly_vgp_HiC_2.0/evaluation/merqury/bPasAmo1_png/
pacbio_read_dir: s3://genomeark/species/Passerina_amoena/bPasAmo1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Passerina_amoena/bPasAmo1/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)
  - VGP9 decontamination unpublished workflow using FCS (v0.5.5+galaxy0)
  - Pre-curation worklfow (v1.0beta6)
notes: This was a Hifiasm-HiC assembly of bPasAmo1 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.