Eidolon dupreanum

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mEidDup1 104.59 Gbp N/A 47.0 GiB
PacBio HiFi (.bam) mEidDup1 107.00 Gbp N/A 347.1 GiB
Arima mEidDup1 238.37 Gbp N/A 120.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 10 June 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mEidDup1 PacBio HiFi (.fq) 104.59 Gbp N/A 47.0 GiB
PacBio HiFi (.bam) 107.00 Gbp N/A 347.1 GiB
Arima 238.37 Gbp N/A 120.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 10 June 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 17 September 2025
mEidDup1.HiC.hap1.20250917.fasta.gz (532.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 112.13 Mbp 1 363.33 Mbp
20 4 88.13 Mbp 2 252.05 Mbp
30 7 77.02 Mbp 2 252.05 Mbp
40 10 73.57 Mbp 3 214.41 Mbp
50 13 52.32 Mbp 4 196.24 Mbp
60 17 45.54 Mbp 6 147.85 Mbp
70 22 37.91 Mbp 7 135.74 Mbp
80 28 27.16 Mbp 8 118.93 Mbp
90 36 16.94 Mbp 10 104.87 Mbp
100 183 15.31 Kbp 85 15.31 Kbp
1.000x 183 1.99 Gbp 85 1.99 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 17 September 2025
mEidDup1.HiC.hap2.20250917.fasta.gz (534.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 89.16 Mbp 1 0.53 Gbp
20 5 87.51 Mbp 1 0.53 Gbp
30 7 81.95 Mbp 2 269.58 Mbp
40 10 78.32 Mbp 2 269.58 Mbp
50 12 76.65 Mbp 3 261.98 Mbp
60 15 64.43 Mbp 4 175.68 Mbp
70 19 47.47 Mbp 6 128.19 Mbp
80 24 31.58 Mbp 7 118.82 Mbp
90 33 18.09 Mbp 9 86.56 Mbp
100 136 18.06 Kbp 62 18.06 Kbp
1.000x 136 1.99 Gbp 62 1.99 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 17 September 2025
mEidDup1.MT.20250917.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mEidDup1.yml (view)
species: Eidolon dupreanum
specimem: mEidDup1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Eidolon_dupreanum/mEidDup1/assembly_vgp_HiC_2.0/mEidDup1.HiC.hap1.20250917.fasta.gz
hap2: s3://genomeark/species/Eidolon_dupreanum/mEidDup1/assembly_vgp_HiC_2.0/mEidDup1.HiC.hap2.20250917.fasta.gz
pretext_hap1: s3://genomeark/species/Eidolon_dupreanum/mEidDup1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mEidDup1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Eidolon_dupreanum/mEidDup1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mEidDup1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Eidolon_dupreanum/mEidDup1/assembly_vgp_HiC_2.0/evaluation/merqury/mEidDup1_png/
pacbio_read_dir: s3://genomeark/species/Eidolon_dupreanum/mEidDup1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Eidolon_dupreanum/mEidDup1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.12)
  - VGP8 HiC scaffolding workflow (v2.2) with mapq=10
  - VGP9 decontamination workflow (v0.7) with database PlusPF 2022
  - Pre-curation worklfow (v1.0beta6) with mapq=20
notes: This was a Hifiasm-HiC assembly of mEidDup1 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.