Setophaga coronata

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bSetCor1 94.37 Gbp N/A 41.6 GiB
PacBio HiFi (.bam) bSetCor1 96.39 Gbp N/A 312.0 GiB
Arima bSetCor1 73.22 Gbp N/A 40.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 20 November 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bSetCor1 PacBio HiFi (.fq) 94.37 Gbp N/A 41.6 GiB
PacBio HiFi (.bam) 96.39 Gbp N/A 312.0 GiB
Arima 73.22 Gbp N/A 40.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 20 November 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 9 December 2025
bSetCor1.HiC.hap1.20251209.fasta.gz (303.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 64.42 Mbp 1 160.26 Mbp
20 5 51.77 Mbp 2 122.64 Mbp
30 7 42.90 Mbp 3 119.31 Mbp
40 10 37.48 Mbp 5 78.06 Mbp
50 14 31.39 Mbp 6 74.28 Mbp
60 18 23.96 Mbp 8 48.76 Mbp
70 25 13.35 Mbp 11 39.72 Mbp
80 35 9.10 Mbp 15 21.85 Mbp
90 53 5.29 Mbp 22 14.10 Mbp
100 240 4.99 Kbp 118 4.99 Kbp
1.000x 240 1.22 Gbp 118 1.22 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 9 December 2025
bSetCor1.HiC.hap2.20251209.fasta.gz (302.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 85.74 Mbp 1 160.49 Mbp
20 3 68.75 Mbp 2 123.73 Mbp
30 5 53.99 Mbp 3 120.01 Mbp
40 8 38.21 Mbp 5 74.22 Mbp
50 12 29.36 Mbp 6 65.68 Mbp
60 17 22.92 Mbp 9 37.92 Mbp
70 23 16.59 Mbp 13 27.55 Mbp
80 32 10.82 Mbp 18 21.76 Mbp
90 48 5.84 Mbp 25 13.89 Mbp
100 249 15.72 Kbp 122 15.72 Kbp
1.000x 249 1.21 Gbp 122 1.21 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 9 December 2025
bSetCor1.MT.20251209.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bSetCor1.yml (view)
species: Setophaga coronata
specimem: bSetCor1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Setophaga_coronata/bSetCor1/assembly_vgp_HiC_2.0/bSetCor1.HiC.hap1.20251209.fasta.gz
hap2: s3://genomeark/species/Setophaga_coronata/bSetCor1/assembly_vgp_HiC_2.0/bSetCor1.HiC.hap2.20251209.fasta.gz
pretext_hap1: s3://genomeark/species/Setophaga_coronata/bSetCor1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bSetCor1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Setophaga_coronata/bSetCor1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bSetCor1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Setophaga_coronata/bSetCor1/assembly_vgp_HiC_2.0/evaluation/merqury/bSetCor1_png/
pacbio_read_dir: s3://genomeark/species/Setophaga_coronata/bSetCor1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Setophaga_coronata/bSetCor1/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 (v3.2) with mapq=10
  - VGP9 decontamination workflow (v1.2) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of bSetCor1 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.