Drepanis coccinea

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bDreCoc1 58.27 Gbp N/A 27.1 GiB
PacBio HiFi (.bam) bDreCoc1 59.52 Gbp N/A 195.0 GiB
Arima bDreCoc1 63.79 Gbp N/A 34.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 15 April 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bDreCoc1 PacBio HiFi (.fq) 58.27 Gbp N/A 27.1 GiB
PacBio HiFi (.bam) 59.52 Gbp N/A 195.0 GiB
Arima 63.79 Gbp N/A 34.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 15 April 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 20 April 2026
bDreCoc1.HiC.hap1.20260420.fasta.gz (305.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 62.74 Mbp 1 155.29 Mbp
20 5 42.25 Mbp 2 119.17 Mbp
30 8 31.70 Mbp 3 117.81 Mbp
40 13 22.54 Mbp 5 73.27 Mbp
50 19 19.81 Mbp 7 62.31 Mbp
60 26 16.84 Mbp 10 35.78 Mbp
70 35 11.03 Mbp 15 21.91 Mbp
80 49 7.99 Mbp 21 17.83 Mbp
90 73 3.09 Mbp 33 8.07 Mbp
100 354 16.86 Kbp 184 16.86 Kbp
1.000x 354 1.29 Gbp 184 1.29 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 20 April 2026
bDreCoc1.HiC.hap2.20260420.fasta.gz (298.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 47.95 Mbp 1 154.03 Mbp
20 6 32.43 Mbp 2 119.81 Mbp
30 9 29.98 Mbp 3 118.01 Mbp
40 14 24.79 Mbp 5 73.76 Mbp
50 19 19.72 Mbp 6 63.36 Mbp
60 26 16.74 Mbp 9 38.54 Mbp
70 34 11.65 Mbp 12 26.87 Mbp
80 46 8.18 Mbp 18 19.68 Mbp
90 68 3.49 Mbp 26 11.08 Mbp
100 324 16.94 Kbp 157 16.94 Kbp
1.000x 324 1.21 Gbp 157 1.21 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/bDreCoc1.yml (view)
species: Drepanis coccinea
specimen: bDreCoc1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Drepanis_coccinea/bDreCoc1/assembly_vgp_HiC_2.0/bDreCoc1.HiC.hap1.20260420.fasta.gz
hap2: s3://genomeark/species/Drepanis_coccinea/bDreCoc1/assembly_vgp_HiC_2.0/bDreCoc1.HiC.hap2.20260420.fasta.gz
pretext_hap1: s3://genomeark/species/Drepanis_coccinea/bDreCoc1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bDreCoc1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Drepanis_coccinea/bDreCoc1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bDreCoc1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Drepanis_coccinea/bDreCoc1/assembly_vgp_HiC_2.0/evaluation/merqury/bDreCoc1_png/
pacbio_read_dir: s3://genomeark/species/Drepanis_coccinea/bDreCoc1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Drepanis_coccinea/bDreCoc1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy3)
  - yahs (0.25.0+galaxy3)
  - 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)
  - VGP6b purge hap1 (v0.8.5)
  - Pre-curation workflow (v20260330 update) with mapq=10, remove HiC duplicates and generate high-resolution map
notes: This was a Hifiasm-HiC assembly of bDreCoc1 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.