Vireo griseus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bVirGri1 79.95 Gbp N/A 35.9 GiB
PacBio HiFi (.bam) bVirGri1 83.00 Gbp N/A 254.9 GiB
Arima bVirGri1 125.22 Gbp N/A 66.2 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
bVirGri1 PacBio HiFi (.fq) 79.95 Gbp N/A 35.9 GiB
PacBio HiFi (.bam) 83.00 Gbp N/A 254.9 GiB
Arima 125.22 Gbp N/A 66.2 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 26 September 2025
bVirGri1.HiC.hap1.20250926.fasta.gz (343.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 21.09 Mbp 1 160.14 Mbp
20 13 17.07 Mbp 2 119.11 Mbp
30 22 13.13 Mbp 3 118.15 Mbp
40 33 10.92 Mbp 5 76.69 Mbp
50 46 8.58 Mbp 7 67.79 Mbp
60 65 6.19 Mbp 10 33.51 Mbp
70 90 4.41 Mbp 15 21.49 Mbp
80 135 2.24 Mbp 23 11.96 Mbp
90 219 1.12 Mbp 46 2.24 Mbp
100 846 7.87 Kbp 443 7.87 Kbp
1.000x 846 1.32 Gbp 443 1.32 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 26 September 2025
bVirGri1.HiC.hap2.20250926.fasta.gz (292.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 23.99 Mbp 1 159.69 Mbp
20 10 18.80 Mbp 2 121.24 Mbp
30 16 15.96 Mbp 3 118.72 Mbp
40 23 13.86 Mbp 4 76.74 Mbp
50 33 10.44 Mbp 6 67.45 Mbp
60 45 8.10 Mbp 8 37.87 Mbp
70 61 6.00 Mbp 11 24.63 Mbp
80 89 2.85 Mbp 16 20.25 Mbp
90 145 1.37 Mbp 25 7.39 Mbp
100 533 11.40 Kbp 245 11.40 Kbp
1.000x 533 1.11 Gbp 245 1.11 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 26 September 2025
bVirGri1.MT.20250926.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bVirGri1.yml (view)
species: Vireo griseus
specimem: bVirGri1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Vireo_griseus/bVirGri1/assembly_vgp_HiC_2.0/bVirGri1.HiC.hap1.20250926.fasta.gz
hap2: s3://genomeark/species/Vireo_griseus/bVirGri1/assembly_vgp_HiC_2.0/bVirGri1.HiC.hap2.20250926.fasta.gz
pretext_hap1: s3://genomeark/species/Vireo_griseus/bVirGri1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bVirGri1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Vireo_griseus/bVirGri1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bVirGri1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Vireo_griseus/bVirGri1/assembly_vgp_HiC_2.0/evaluation/merqury/bVirGri1_png/
pacbio_read_dir: s3://genomeark/species/Vireo_griseus/bVirGri1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Vireo_griseus/bVirGri1/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 (0.5.0+galaxy0) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of bVirGri1 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.