Setophaga citrina

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bSetCit1 78.26 Gbp N/A 34.5 GiB
PacBio HiFi (.bam) bSetCit1 80.03 Gbp N/A 257.4 GiB
Arima bSetCit1 73.06 Gbp N/A 41.0 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
bSetCit1 PacBio HiFi (.fq) 78.26 Gbp N/A 34.5 GiB
PacBio HiFi (.bam) 80.03 Gbp N/A 257.4 GiB
Arima 73.06 Gbp N/A 41.0 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
bSetCit1.HiC.hap1.20251209.fasta.gz (341.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 56.24 Mbp 2 103.44 Mbp
20 6 47.25 Mbp 4 86.28 Mbp
30 10 35.80 Mbp 6 64.69 Mbp
40 16 20.39 Mbp 9 55.07 Mbp
50 27 13.42 Mbp 15 21.83 Mbp
60 46 6.56 Mbp 24 14.99 Mbp
70 102 1.86 Mbp 43 2.79 Mbp
80 251 0.77 Mbp 168 0.89 Mbp
90 797 157.57 Kbp 654 167.03 Kbp
100 3264 12.86 Kbp 3077 12.86 Kbp
1.000x 3264 1.73 Gbp 3077 1.73 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 9 December 2025
bSetCit1.HiC.hap2.20251209.fasta.gz (328.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 53.60 Mbp 2 122.30 Mbp
20 5 52.12 Mbp 3 98.42 Mbp
30 9 38.46 Mbp 4 86.27 Mbp
40 13 28.83 Mbp 6 64.62 Mbp
50 19 20.98 Mbp 9 44.23 Mbp
60 26 15.56 Mbp 12 33.59 Mbp
70 38 9.54 Mbp 18 20.20 Mbp
80 58 4.39 Mbp 27 11.93 Mbp
90 113 1.47 Mbp 46 2.92 Mbp
100 988 17.57 Kbp 777 17.57 Kbp
1.000x 988 1.38 Gbp 777 1.38 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 9 December 2025
bSetCit1.MT.20251209.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bSetCit1.yml (view)
species: Setophaga citrina
specimem: bSetCit1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Setophaga_citrina/bSetCit1/assembly_vgp_HiC_2.0/bSetCit1.HiC.hap1.20251209.fasta.gz
hap2: s3://genomeark/species/Setophaga_citrina/bSetCit1/assembly_vgp_HiC_2.0/bSetCit1.HiC.hap2.20251209.fasta.gz
pretext_hap1: s3://genomeark/species/Setophaga_citrina/bSetCit1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bSetCit1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Setophaga_citrina/bSetCit1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bSetCit1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Setophaga_citrina/bSetCit1/assembly_vgp_HiC_2.0/evaluation/merqury/bSetCit1_png/
pacbio_read_dir: s3://genomeark/species/Setophaga_citrina/bSetCit1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Setophaga_citrina/bSetCit1/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 bSetCit1 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.