Setophaga pinus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bSetPin1 63.20 Gbp N/A 27.5 GiB
PacBio HiFi (.bam) bSetPin1 64.94 Gbp N/A 212.2 GiB
Arima bSetPin1 63.31 Gbp N/A 34.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 5 January 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bSetPin1 PacBio HiFi (.fq) 63.20 Gbp N/A 27.5 GiB
PacBio HiFi (.bam) 64.94 Gbp N/A 212.2 GiB
Arima 63.31 Gbp N/A 34.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 5 January 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 11 February 2026
bSetPin1.HiC.hap1.20260211.fasta.gz (321.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 43.89 Mbp 1 160.66 Mbp
20 6 33.28 Mbp 2 121.43 Mbp
30 10 28.15 Mbp 3 118.45 Mbp
40 15 21.74 Mbp 5 75.19 Mbp
50 21 20.02 Mbp 7 67.17 Mbp
60 29 13.09 Mbp 9 43.59 Mbp
70 40 9.33 Mbp 12 36.96 Mbp
80 59 5.51 Mbp 17 23.55 Mbp
90 90 2.59 Mbp 23 15.78 Mbp
100 433 11.58 Kbp 211 11.58 Kbp
1.000x 433 1.28 Gbp 211 1.28 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 11 February 2026
bSetPin1.HiC.hap2.20260211.fasta.gz (308.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 36.03 Mbp 1 157.61 Mbp
20 7 29.80 Mbp 2 122.40 Mbp
30 12 24.02 Mbp 3 118.21 Mbp
40 17 21.85 Mbp 5 74.95 Mbp
50 23 18.48 Mbp 6 73.93 Mbp
60 31 12.14 Mbp 8 42.80 Mbp
70 43 7.56 Mbp 11 38.83 Mbp
80 63 5.02 Mbp 16 21.33 Mbp
90 97 2.39 Mbp 23 13.72 Mbp
100 325 16.82 Kbp 118 16.82 Kbp
1.000x 325 1.22 Gbp 118 1.22 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 11 February 2026
bSetPin1.MT.20260211.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bSetPin1.yml (view)
species: Setophaga pinus
specimem: bSetPin1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Setophaga_pinus/bSetPin1/assembly_vgp_HiC_2.0/bSetPin1.HiC.hap1.20260211.fasta.gz
hap2: s3://genomeark/species/Setophaga_pinus/bSetPin1/assembly_vgp_HiC_2.0/bSetPin1.HiC.hap2.20260211.fasta.gz
pretext_hap1: s3://genomeark/species/Setophaga_pinus/bSetPin1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bSetPin1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Setophaga_pinus/bSetPin1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bSetPin1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Setophaga_pinus/bSetPin1/assembly_vgp_HiC_2.0/evaluation/merqury/bSetPin1_png/
pacbio_read_dir: s3://genomeark/species/Setophaga_pinus/bSetPin1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Setophaga_pinus/bSetPin1/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 bSetPin1 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.