Piranga ludoviciana

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bPirLud1 80.17 Gbp N/A 36.6 GiB
PacBio HiFi (.bam) bPirLud1 83.06 Gbp N/A 271.1 GiB
Arima bPirLud1 138.05 Gbp N/A 72.0 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
bPirLud1 PacBio HiFi (.fq) 80.17 Gbp N/A 36.6 GiB
PacBio HiFi (.bam) 83.06 Gbp N/A 271.1 GiB
Arima 138.05 Gbp N/A 72.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 31 October 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 10 November 2025
bPirLud1.HiC.hap1.20251110.fasta.gz (284.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 144.46 Mbp 1 155.94 Mbp
20 2 113.33 Mbp 2 117.26 Mbp
30 3 104.03 Mbp 3 115.62 Mbp
40 5 57.76 Mbp 4 75.06 Mbp
50 8 34.30 Mbp 6 64.89 Mbp
60 12 23.39 Mbp 8 37.74 Mbp
70 17 19.49 Mbp 12 23.56 Mbp
80 24 11.93 Mbp 17 17.48 Mbp
90 38 5.59 Mbp 25 11.93 Mbp
100 250 7.93 Kbp 121 7.93 Kbp
1.000x 250 1.11 Gbp 121 1.11 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 10 November 2025
bPirLud1.HiC.hap2.20251110.fasta.gz (312.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 95.57 Mbp 1 155.53 Mbp
20 3 88.77 Mbp 2 117.21 Mbp
30 4 75.01 Mbp 3 115.80 Mbp
40 7 49.44 Mbp 5 75.01 Mbp
50 9 41.78 Mbp 6 73.71 Mbp
60 13 26.56 Mbp 9 38.33 Mbp
70 18 17.72 Mbp 13 24.38 Mbp
80 26 13.87 Mbp 18 19.34 Mbp
90 38 6.97 Mbp 26 9.90 Mbp
100 247 11.96 Kbp 124 11.96 Kbp
1.000x 247 1.22 Gbp 124 1.22 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 10 November 2025
bPirLud1.MT.20251110.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bPirLud1.yml (view)
species: Piranga ludoviciana
specimem: bPirLud1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Piranga_ludoviciana/bPirLud1/assembly_vgp_HiC_2.0/bPirLud1.HiC.hap1.20251110.fasta.gz
hap2: s3://genomeark/species/Piranga_ludoviciana/bPirLud1/assembly_vgp_HiC_2.0/bPirLud1.HiC.hap2.20251110.fasta.gz
pretext_hap1: s3://genomeark/species/Piranga_ludoviciana/bPirLud1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bPirLud1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Piranga_ludoviciana/bPirLud1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bPirLud1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Piranga_ludoviciana/bPirLud1/assembly_vgp_HiC_2.0/evaluation/merqury/bPirLud1_png/
pacbio_read_dir: s3://genomeark/species/Piranga_ludoviciana/bPirLud1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Piranga_ludoviciana/bPirLud1/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 bPirLud1 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.