Pteropus rufus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mPteRuf1 164.20 Gbp N/A 76.3 GiB
PacBio HiFi (.bam) mPteRuf1 166.56 Gbp N/A 533.1 GiB
Arima mPteRuf1 173.72 Gbp N/A 89.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 24 June 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mPteRuf1 PacBio HiFi (.fq) 164.20 Gbp N/A 76.3 GiB
PacBio HiFi (.bam) 166.56 Gbp N/A 533.1 GiB
Arima 173.72 Gbp N/A 89.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 24 June 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 6 October 2025
mPteRuf1.HiC.hap1.20251006.fasta.gz (544.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 99.72 Mbp 2 183.38 Mbp
20 5 71.82 Mbp 3 181.95 Mbp
30 8 64.00 Mbp 4 170.47 Mbp
40 12 54.80 Mbp 5 130.98 Mbp
50 16 50.99 Mbp 7 120.03 Mbp
60 20 44.23 Mbp 9 118.24 Mbp
70 25 34.26 Mbp 11 104.33 Mbp
80 33 22.18 Mbp 13 87.14 Mbp
90 45 12.73 Mbp 15 65.81 Mbp
100 241 16.85 Kbp 175 16.85 Kbp
1.000x 241 2.09 Gbp 175 2.09 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 6 October 2025
mPteRuf1.HiC.hap2.20251006.fasta.gz (538.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 107.55 Mbp 2 182.83 Mbp
20 5 79.77 Mbp 3 176.83 Mbp
30 7 69.43 Mbp 4 168.87 Mbp
40 11 62.78 Mbp 5 129.70 Mbp
50 14 46.70 Mbp 7 121.14 Mbp
60 19 42.64 Mbp 9 118.90 Mbp
70 24 32.52 Mbp 10 106.62 Mbp
80 32 23.75 Mbp 12 99.71 Mbp
90 43 13.11 Mbp 15 65.97 Mbp
100 181 34.59 Kbp 102 34.59 Kbp
1.000x 181 2.04 Gbp 102 2.04 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 6 October 2025
mPteRuf1.MT.20251006.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mPteRuf1.yml (view)
species: Pteropus rufus
specimem: mPteRuf1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Pteropus_rufus/mPteRuf1/assembly_vgp_HiC_2.0/mPteRuf1.HiC.hap1.20251006.fasta.gz
hap2: s3://genomeark/species/Pteropus_rufus/mPteRuf1/assembly_vgp_HiC_2.0/mPteRuf1.HiC.hap2.20251006.fasta.gz
pretext_hap1: s3://genomeark/species/Pteropus_rufus/mPteRuf1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mPteRuf1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Pteropus_rufus/mPteRuf1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mPteRuf1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Pteropus_rufus/mPteRuf1/assembly_vgp_HiC_2.0/evaluation/merqury/mPteRuf1_png/
pacbio_read_dir: s3://genomeark/species/Pteropus_rufus/mPteRuf1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Pteropus_rufus/mPteRuf1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.4)
  - VGP1 genomic profiling workflow (v0.2.2)
  - VGP4 HiFi HiC assembly workflow (v0.3.12)
  - VGP8 HiC scaffolding workflow (v2.2) with mapq=10
  - VGP9 decontamination workflow unpublished using FCS (0.5.5+galaxy0) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of mPteRuf1 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.