Rhinolophus hildebrandtii

Hildebrandt's horseshoe bat

Included in the VGP and BAT1K.

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


metadata.yaml (view) (edit on github)
species:
  short_name: mRhiHil
  name: Rhinolophus hildebrandtii
  taxon_id: 302411
  common_name: Hildebrandt's horseshoe bat
  order:
    name: Chiroptera
  family:
    name: Rhinolophidae
  individuals:
    - short_name: mRhiHil1
  genome_size: 2102700000
  genome_size_method: GoaT
  project: [ vgp , bat1k ]
No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mRhiHil1 34.66 Gbp 16.49x 123.0 GiB
PacBio HiFi (.bam) mRhiHil1 145.04 Gbp 68.98x 514.6 GiB
Arima mRhiHil1 211.25 Gbp 100.47x 93.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.10 Gbp.
Last upload on 9 April 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mRhiHil1 PacBio HiFi (.fq) 34.66 Gbp 16.49x 123.0 GiB
PacBio HiFi (.bam) 145.04 Gbp 68.98x 514.6 GiB
Arima 211.25 Gbp 100.47x 93.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.10 Gbp.
Last upload on 9 April 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 10 July 2025
mRhiHil1.HiC.hap1.20250710.fasta.gz (544.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 109.38 Mbp 2 164.69 Mbp
20 4 103.83 Mbp 3 112.29 Mbp
30 7 85.80 Mbp 5 109.38 Mbp
40 9 78.96 Mbp 7 103.07 Mbp
50 12 67.90 Mbp 9 95.14 Mbp
60 15 60.75 Mbp 11 90.52 Mbp
70 19 50.96 Mbp 14 74.46 Mbp
80 24 32.16 Mbp 17 64.06 Mbp
90 32 19.35 Mbp 21 47.17 Mbp
100 0 0
0.967x 165 2.03 Gbp 74 2.03 Gbp
NG based on genome size 2.10 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 10 July 2025
mRhiHil1.HiC.hap2.20250710.fasta.gz (585.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 108.47 Mbp 1 324.47 Mbp
20 4 103.76 Mbp 2 203.65 Mbp
30 6 101.82 Mbp 3 163.96 Mbp
40 9 74.30 Mbp 4 155.07 Mbp
50 12 66.82 Mbp 6 121.09 Mbp
60 15 64.88 Mbp 8 109.41 Mbp
70 19 51.69 Mbp 10 103.76 Mbp
80 23 41.17 Mbp 12 101.07 Mbp
90 29 30.88 Mbp 14 78.27 Mbp
100 40 6.61 Mbp 17 64.88 Mbp
1.044x 160 2.20 Gbp 63 2.20 Gbp
NG based on genome size 2.10 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 10 July 2025
mRhiHil1.MT.20250710.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mRhiHil1.yml (view)
species: Rhinolophus hildebrandtii
specimem: mRhiHil1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: HiC signals are not sufficient for curation.
hap1: s3://genomeark/species/Rhinolophus_hildebrandtii/mRhiHil1/assembly_vgp_HiC_2.0/mRhiHil1.HiC.hap1.20250710.fasta.gz
hap2: s3://genomeark/species/Rhinolophus_hildebrandtii/mRhiHil1/assembly_vgp_HiC_2.0/mRhiHil1.HiC.hap2.20250710.fasta.gz
pretext_hap1: s3://genomeark/species/Rhinolophus_hildebrandtii/mRhiHil1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mRhiHil1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Rhinolophus_hildebrandtii/mRhiHil1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mRhiHil1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Rhinolophus_hildebrandtii/mRhiHil1/assembly_vgp_HiC_2.0/evaluation/merqury/mRhiHil1_png/
pacbio_read_dir: s3://genomeark/species/Rhinolophus_hildebrandtii/mRhiHil1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Rhinolophus_hildebrandtii/mRhiHil1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.1)
  - VGP1 genomic profiling workflow (v0.2)
  - VGP4 HiFi HiC assembly workflow (v0.3.6) re-run compleasm with correct input for hap2
  - VGP8 HiC scaffolding workflow (v1.8)
notes: This was a Hifiasm-HiC assembly of mRhiHil1 resulting in two haplotype assemblies. The new 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. The old HiC data used Arima v1 kit and does not require trimming. The assembly used the new HiC data only.
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.