Pipilo erythrophthalmus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bPipEry1 73.83 Gbp N/A 33.3 GiB
PacBio HiFi (.bam) bPipEry1 77.23 Gbp N/A 251.8 GiB
Arima bPipEry1 84.26 Gbp N/A 45.8 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
bPipEry1 PacBio HiFi (.fq) 73.83 Gbp N/A 33.3 GiB
PacBio HiFi (.bam) 77.23 Gbp N/A 251.8 GiB
Arima 84.26 Gbp N/A 45.8 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 26 September 2025
bPipEry1.HiC.hap1.20250926.fasta.gz (324.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 52.63 Mbp 1 155.53 Mbp
20 5 49.27 Mbp 2 117.85 Mbp
30 8 41.21 Mbp 4 84.52 Mbp
40 12 31.34 Mbp 5 73.73 Mbp
50 16 26.15 Mbp 7 56.88 Mbp
60 22 19.18 Mbp 11 26.15 Mbp
70 32 10.19 Mbp 16 20.41 Mbp
80 50 5.53 Mbp 25 10.87 Mbp
90 101 0.98 Mbp 40 4.65 Mbp
100 953 11.27 Kbp 826 11.27 Kbp
1.000x 953 1.32 Gbp 826 1.32 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 26 September 2025
bPipEry1.HiC.hap2.20250926.fasta.gz (327.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 60.74 Mbp 1 155.41 Mbp
20 5 50.72 Mbp 3 115.91 Mbp
30 9 32.49 Mbp 4 74.87 Mbp
40 14 24.25 Mbp 6 64.57 Mbp
50 20 19.30 Mbp 9 34.31 Mbp
60 30 10.90 Mbp 14 23.48 Mbp
70 46 6.14 Mbp 23 12.72 Mbp
80 84 2.30 Mbp 36 7.87 Mbp
90 213 0.60 Mbp 119 0.78 Mbp
100 1013 11.68 Kbp 857 11.68 Kbp
1.000x 1013 1.42 Gbp 857 1.42 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 26 September 2025
bPipEry1.MT.20250926.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bPipEry1.yml (view)
species: Pipilo erythrophthalmus
specimem: bPipEry1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Pipilo_erythrophthalmus/bPipEry1/assembly_vgp_HiC_2.0/bPipEry1.HiC.hap1.20250926.fasta.gz
hap2: s3://genomeark/species/Pipilo_erythrophthalmus/bPipEry1/assembly_vgp_HiC_2.0/bPipEry1.HiC.hap2.20250926.fasta.gz
pretext_hap1: s3://genomeark/species/Pipilo_erythrophthalmus/bPipEry1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bPipEry1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Pipilo_erythrophthalmus/bPipEry1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bPipEry1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Pipilo_erythrophthalmus/bPipEry1/assembly_vgp_HiC_2.0/evaluation/merqury/bPipEry1_png/
pacbio_read_dir: s3://genomeark/species/Pipilo_erythrophthalmus/bPipEry1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Pipilo_erythrophthalmus/bPipEry1/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 (v1.0bbeta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of bPipEry1 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.