Chlorodrepanis virens

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bHemVir1 63.43 Gbp N/A 28.8 GiB
PacBio HiFi (.bam) bHemVir1 64.28 Gbp N/A 210.8 GiB
Arima bHemVir1 52.05 Gbp N/A 27.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 26 March 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bHemVir1 PacBio HiFi (.fq) 63.43 Gbp N/A 28.8 GiB
PacBio HiFi (.bam) 64.28 Gbp N/A 210.8 GiB
Arima 52.05 Gbp N/A 27.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 26 March 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 15 April 2026
bHemVir1.HiC.hap1.20260415.fasta.gz (292.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 51.19 Mbp 1 156.75 Mbp
20 5 42.30 Mbp 2 118.79 Mbp
30 8 34.66 Mbp 3 117.49 Mbp
40 12 26.42 Mbp 4 83.73 Mbp
50 17 20.42 Mbp 6 72.72 Mbp
60 23 17.94 Mbp 7 63.59 Mbp
70 29 15.25 Mbp 10 30.47 Mbp
80 39 10.00 Mbp 15 20.42 Mbp
90 55 5.17 Mbp 22 12.17 Mbp
100 356 17.12 Kbp 143 17.12 Kbp
1.000x 356 1.13 Gbp 143 1.13 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 15 April 2026
bHemVir1.HiC.hap2.20260415.fasta.gz (297.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 57.79 Mbp 1 155.93 Mbp
20 4 49.52 Mbp 2 118.37 Mbp
30 6 36.25 Mbp 3 118.00 Mbp
40 10 31.10 Mbp 4 82.95 Mbp
50 15 20.05 Mbp 6 72.97 Mbp
60 21 18.80 Mbp 8 49.49 Mbp
70 29 12.43 Mbp 11 31.10 Mbp
80 40 8.11 Mbp 15 19.66 Mbp
90 59 4.14 Mbp 23 12.43 Mbp
100 343 21.07 Kbp 131 30.59 Kbp
1.000x 343 1.15 Gbp 131 1.15 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 17 April 2026
bHemVir1.MT.20260417.fasta.gz (5.0 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bHemVir1.yml (view)
species: Chlorodrepanis virens
specimen: bHemVir1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Chlorodrepanis_virens/bHemVir1/assembly_vgp_HiC_2.0/bHemVir1.HiC.hap1.20260415.fasta.gz
hap2: s3://genomeark/species/Chlorodrepanis_virens/bHemVir1/assembly_vgp_HiC_2.0/bHemVir1.HiC.hap2.20260415.fasta.gz
pretext_hap1: s3://genomeark/species/Chlorodrepanis_virens/bHemVir1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bHemVir1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Chlorodrepanis_virens/bHemVir1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bHemVir1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Chlorodrepanis_virens/bHemVir1/assembly_vgp_HiC_2.0/evaluation/merqury/bHemVir1_png/
pacbio_read_dir: s3://genomeark/species/Chlorodrepanis_virens/bHemVir1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Chlorodrepanis_virens/bHemVir1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy3)
  - yahs (1.2a.2+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)
  - 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 bHemVir1 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. There are many NUMT reads in the raw HiFi data. Among these, eight HiFi reads are mapped with mapping quality of 60 to the reference KM078788.1 mitogenome (the reference was duplicated so the entire HiFi reads can be mapped onto). Picked two reads that appear to be the most similar to KM078788.1 mitogenome and generated a consensus mitochondrial sequence.
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.