Puffinus subalaris

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bPufSub1 104.62 Gbp N/A 48.0 GiB
PacBio HiFi (.bam) bPufSub1 106.55 Gbp N/A 353.4 GiB
Arima bPufSub1 108.83 Gbp N/A 58.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 13 February 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bPufSub1 PacBio HiFi (.fq) 104.62 Gbp N/A 48.0 GiB
PacBio HiFi (.bam) 106.55 Gbp N/A 353.4 GiB
Arima 108.83 Gbp N/A 58.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 13 February 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 20 March 2026
bPufSub1.HiC.hap1.20260320.fasta.gz (342.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 161.52 Mbp 1 222.38 Mbp
20 2 154.91 Mbp 2 171.71 Mbp
30 3 129.08 Mbp 3 130.52 Mbp
40 4 88.79 Mbp 4 88.79 Mbp
50 7 43.55 Mbp 5 88.47 Mbp
60 11 27.29 Mbp 7 46.01 Mbp
70 17 22.67 Mbp 11 27.29 Mbp
80 24 15.81 Mbp 16 23.13 Mbp
90 35 9.65 Mbp 23 14.67 Mbp
100 254 9.90 Kbp 168 9.90 Kbp
1.000x 254 1.32 Gbp 168 1.32 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 20 March 2026
bPufSub1.HiC.hap2.20260320.fasta.gz (342.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 174.27 Mbp 1 222.24 Mbp
20 2 170.70 Mbp 2 172.04 Mbp
30 3 66.90 Mbp 3 130.36 Mbp
40 6 44.83 Mbp 4 88.95 Mbp
50 9 39.72 Mbp 5 88.20 Mbp
60 12 32.27 Mbp 7 45.45 Mbp
70 17 23.45 Mbp 11 27.47 Mbp
80 24 15.76 Mbp 16 23.00 Mbp
90 34 9.49 Mbp 24 11.31 Mbp
100 223 15.86 Kbp 160 15.86 Kbp
1.000x 223 1.32 Gbp 160 1.32 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rcokefeller from 19 March 2026
bPufSub1.MT.20260319.fasta.gz (5.5 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bPufSub1.yml (view)
species: Puffinus subalaris
specimem: bPufSub1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Puffinus_subalaris/bPufSub1/assembly_vgp_HiC_2.0/bPufSub1.HiC.hap1.20260320.fasta.gz
hap2: s3://genomeark/species/Puffinus_subalaris/bPufSub1/assembly_vgp_HiC_2.0/bPufSub1.HiC.hap2.20260320.fasta.gz
pretext_hap1: s3://genomeark/species/Puffinus_subalaris/bPufSub1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bPufSub1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Puffinus_subalaris/bPufSub1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bPufSub1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Puffinus_subalaris/bPufSub1/assembly_vgp_HiC_2.0/evaluation/merqury/bPufSub1_png/
pacbio_read_dir: s3://genomeark/species/Puffinus_subalaris/bPufSub1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Puffinus_subalaris/bPufSub1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.8)
  - VGP4 HiFi HiC assembly workflow (v0.5)
  - VGP8 HiC scaffolding workflow (v3.4) with mapq=10. Note that the HiC duplicates were not removed because samtools markdup tool did not have the flag -r (even if the workflow says it’s removed). 
  - VGP9 decontamination workflow (v1.2) 
  - Pre-curation worklfow (v2.2) with mapq=10, keep HiC duplicates and generate high-resolution map
notes: This was a Hifiasm-HiC assembly of bPufSub1 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.