Butorides sundevalli

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bButSun1 92.17 Gbp N/A 41.9 GiB
PacBio HiFi (.bam) bButSun1 93.58 Gbp N/A 308.2 GiB
Arima bButSun1 40.81 Gbp N/A 21.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 12 March 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bButSun1 PacBio HiFi (.fq) 92.17 Gbp N/A 41.9 GiB
PacBio HiFi (.bam) 93.58 Gbp N/A 308.2 GiB
Arima 40.81 Gbp N/A 21.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 12 March 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 15 April 2026
bButSun1.HiC.hap1.20260415.fasta.gz (335.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 102.53 Mbp 1 220.86 Mbp
20 3 83.38 Mbp 2 168.14 Mbp
30 4 82.39 Mbp 2 168.14 Mbp
40 6 63.80 Mbp 3 129.72 Mbp
50 8 52.27 Mbp 5 83.38 Mbp
60 11 42.96 Mbp 6 82.39 Mbp
70 14 29.80 Mbp 8 52.27 Mbp
80 19 21.76 Mbp 11 41.31 Mbp
90 28 8.52 Mbp 15 23.46 Mbp
100 301 7.70 Kbp 173 7.70 Kbp
1.000x 301 1.26 Gbp 173 1.26 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 15 April 2026
bButSun1.HiC.hap2.20260415.fasta.gz (332.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 102.56 Mbp 1 219.39 Mbp
20 3 86.56 Mbp 2 168.18 Mbp
30 4 84.23 Mbp 2 168.18 Mbp
40 6 63.91 Mbp 3 129.87 Mbp
50 9 44.19 Mbp 5 84.23 Mbp
60 12 39.22 Mbp 6 83.92 Mbp
70 15 26.31 Mbp 8 51.38 Mbp
80 22 14.63 Mbp 11 39.22 Mbp
90 32 9.00 Mbp 15 23.30 Mbp
100 304 15.63 Kbp 167 15.63 Kbp
1.000x 304 1.25 Gbp 167 1.25 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 15 April 2026
bButSun1.MT.20260415.fasta.gz (5.7 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bButSun1.yml (view)
species: Butorides sundevalli
specimen: bButSun1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Butorides_sundevalli/bButSun1/assembly_vgp_HiC_2.0/bButSun1.HiC.hap1.20260415.fasta.gz
hap2: s3://genomeark/species/Butorides_sundevalli/bButSun1/assembly_vgp_HiC_2.0/bButSun1.HiC.hap2.20260415.fasta.gz
pretext_hap1: s3://genomeark/species/Butorides_sundevalli/bButSun1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bButSun1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Butorides_sundevalli/bButSun1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bButSun1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Butorides_sundevalli/bButSun1/assembly_vgp_HiC_2.0/evaluation/merqury/bButSun1_png/
pacbio_read_dir: s3://genomeark/species/Butorides_sundevalli/bButSun1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Butorides_sundevalli/bButSun1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy3)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v20260331 update)
  - VGP4 HiFi HiC assembly workflow (v0.6)
  - VGP8 HiC scaffolding workflow (v3.5) with mapq=10
  - VGP9 decontamination workflow (v1.3)
  - Pre-curation workflow (v20260330 update) with mapq=10, keep HiC duplicates and generate standard pretextmap (not high-resolution)
notes: This was a Hifiasm-HiC assembly of bButSun1 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.