Poecile gambeli

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bPoeGam1 70.24 Gbp N/A 31.6 GiB
PacBio HiFi (.bam) bPoeGam1 71.30 Gbp N/A 232.1 GiB
Arima bPoeGam1 86.77 Gbp N/A 46.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 16 December 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bPoeGam1 PacBio HiFi (.fq) 70.24 Gbp N/A 31.6 GiB
PacBio HiFi (.bam) 71.30 Gbp N/A 232.1 GiB
Arima 86.77 Gbp N/A 46.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 16 December 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 6 February 2026
bPoeGam1.HiC.hap1.20260206.fasta.gz (298.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 35.25 Mbp 1 154.61 Mbp
20 7 32.83 Mbp 2 149.31 Mbp
30 11 28.77 Mbp 3 118.60 Mbp
40 16 23.52 Mbp 4 117.40 Mbp
50 21 20.32 Mbp 5 84.21 Mbp
60 27 18.15 Mbp 7 42.11 Mbp
70 35 12.08 Mbp 11 24.48 Mbp
80 48 7.11 Mbp 16 18.15 Mbp
90 73 2.95 Mbp 25 8.52 Mbp
100 353 9.95 Kbp 124 9.95 Kbp
1.000x 353 1.19 Gbp 124 1.19 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 6 February 2026
bPoeGam1.HiC.hap2.20260206.fasta.gz (295.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 39.34 Mbp 1 154.78 Mbp
20 6 29.25 Mbp 2 150.23 Mbp
30 11 22.35 Mbp 3 118.33 Mbp
40 17 20.39 Mbp 4 117.47 Mbp
50 23 19.35 Mbp 5 79.39 Mbp
60 30 12.81 Mbp 7 41.33 Mbp
70 41 8.64 Mbp 10 32.50 Mbp
80 56 6.72 Mbp 14 22.80 Mbp
90 78 3.68 Mbp 21 10.01 Mbp
100 286 10.07 Kbp 91 10.07 Kbp
1.000x 286 1.16 Gbp 91 1.16 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 6 February 2026
bPoeGam1.MT.20260206.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bPoeGam1.yml (view)
species: Poecile gambeli
specimem: bPoeGam1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Poecile_gambeli/bPoeGam1/assembly_vgp_HiC_2.0/bPoeGam1.HiC.hap1.20260206.fasta.gz
hap2: s3://genomeark/species/Poecile_gambeli/bPoeGam1/assembly_vgp_HiC_2.0/bPoeGam1.HiC.hap2.20260206.fasta.gz
pretext_hap1: s3://genomeark/species/Poecile_gambeli/bPoeGam1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bPoeGam1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Poecile_gambeli/bPoeGam1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bPoeGam1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Poecile_gambeli/bPoeGam1/assembly_vgp_HiC_2.0/evaluation/merqury/bPoeGam1_png/
pacbio_read_dir: s3://genomeark/species/Poecile_gambeli/bPoeGam1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Poecile_gambeli/bPoeGam1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.6)
  - VGP4 HiFi HiC assembly workflow (v0.5)
  - VGP8 HiC scaffolding workflow (v3.3) with mapq=10
  - VGP9 decontamination workflow (v1.2) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of bPoeGam1 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.