Passerella iliaca

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bPasIli2 76.43 Gbp N/A 35.6 GiB
PacBio HiFi (.bam) bPasIli2 78.77 Gbp N/A 258.4 GiB
Arima bPasIli2 115.40 Gbp N/A 58.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 31 October 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bPasIli2 PacBio HiFi (.fq) 76.43 Gbp N/A 35.6 GiB
PacBio HiFi (.bam) 78.77 Gbp N/A 258.4 GiB
Arima 115.40 Gbp N/A 58.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 31 October 2025.
Assemblies
Individual 2 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 4 November 2025
bPasIli2.HiC.hap1.20251104.fasta.gz (408.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 29.25 Mbp 2 118.52 Mbp
20 13 21.29 Mbp 3 117.42 Mbp
30 22 17.61 Mbp 6 73.69 Mbp
40 35 13.52 Mbp 10 38.05 Mbp
50 53 8.51 Mbp 17 20.63 Mbp
60 81 5.08 Mbp 30 12.87 Mbp
70 143 1.83 Mbp 55 3.54 Mbp
80 306 0.82 Mbp 189 0.92 Mbp
90 680 326.59 Kbp 525 357.55 Kbp
100 2365 16.94 Kbp 2120 16.94 Kbp
1.000x 2365 1.92 Gbp 2120 1.92 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 4 November 2025
bPasIli2.HiC.hap2.20251104.fasta.gz (328.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 46.39 Mbp 1 157.31 Mbp
20 6 34.11 Mbp 3 117.81 Mbp
30 11 25.08 Mbp 4 74.07 Mbp
40 17 18.33 Mbp 6 68.74 Mbp
50 27 12.11 Mbp 8 40.02 Mbp
60 40 8.85 Mbp 14 20.63 Mbp
70 60 5.06 Mbp 23 12.81 Mbp
80 108 1.92 Mbp 35 7.79 Mbp
90 264 476.68 Kbp 134 0.61 Mbp
100 1099 10.26 Kbp 879 10.26 Kbp
1.000x 1099 1.38 Gbp 879 1.38 Gbp
NG based on genome size .
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 4 November 2025
bPasIli2.MT.20251104.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bPasIli2.yml (view)
species: Passerella iliaca
specimem: bPasIli2
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Passerella_iliaca/bPasIli2/assembly_vgp_HiC_2.0/bPasIli2.HiC.hap1.20251104.fasta.gz
hap2: s3://genomeark/species/Passerella_iliaca/bPasIli2/assembly_vgp_HiC_2.0/bPasIli2.HiC.hap2.20251104.fasta.gz
pretext_hap1: s3://genomeark/species/Passerella_iliaca/bPasIli2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bPasIli2_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Passerella_iliaca/bPasIli2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bPasIli2_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Passerella_iliaca/bPasIli2/assembly_vgp_HiC_2.0/evaluation/merqury/bPasIli2_png/
pacbio_read_dir: s3://genomeark/species/Passerella_iliaca/bPasIli2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Passerella_iliaca/bPasIli2/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 (v0.4)
  - VGP8 HiC scaffolding workflow (v3.1) with mapq=10
  - VGP9 decontamination workflow (v1.2) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of bPasIli2 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.