Rhinolophus darlingii

Darling'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: mRhiDar
  name: Rhinolophus darlingii
  taxon_id: 49443
  common_name: Darling's horseshoe bat
  order:
    name: Chiroptera
  family:
    name: Rhinolophidae
  individuals:
    - short_name: mRhiDar1
  genome_size: 2278740000
  genome_size_method: GoaT
  project: [ vgp , bat1k ]
No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mRhiDar1 103.79 Gbp 45.55x 84.6 GiB
PacBio HiFi (.bam) mRhiDar1 104.60 Gbp 45.90x 366.4 GiB
Arima mRhiDar1 156.36 Gbp 68.62x 68.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.28 Gbp.
Last upload on 9 April 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mRhiDar1 PacBio HiFi (.fq) 103.79 Gbp 45.55x 84.6 GiB
PacBio HiFi (.bam) 104.60 Gbp 45.90x 366.4 GiB
Arima 156.36 Gbp 68.62x 68.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.28 Gbp.
Last upload on 9 April 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 9 February 2026
mRhiDar1.hap1.cur.20260209.fasta.gz (630.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 101.21 Mbp 2 111.32 Mbp
20 5 95.20 Mbp 4 110.50 Mbp
30 7 88.92 Mbp 7 100.97 Mbp
40 11 64.25 Mbp 9 95.20 Mbp
50 14 58.16 Mbp 11 88.92 Mbp
60 19 52.56 Mbp 14 74.68 Mbp
70 23 45.49 Mbp 18 59.70 Mbp
80 29 31.05 Mbp 22 51.26 Mbp
90 40 9.26 Mbp 27 28.31 Mbp
100 0 0
0.957x 281 2.18 Gbp 222 2.18 Gbp
NG based on genome size 2.28 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 9 February 2026
mRhiDar1.hap2.cur.20260209.fasta.gz (550.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 100.80 Mbp 3 110.20 Mbp
20 5 96.10 Mbp 5 101.91 Mbp
30 7 92.90 Mbp 7 100.80 Mbp
40 10 77.76 Mbp 9 92.90 Mbp
50 13 68.70 Mbp 12 77.76 Mbp
60 17 56.22 Mbp 15 67.07 Mbp
70 21 46.45 Mbp 19 58.17 Mbp
80 28 26.76 Mbp 23 46.45 Mbp
90 208 296.41 Kbp 144 332.40 Kbp
100 0 0
0.935x 926 2.13 Gbp 822 2.13 Gbp
NG based on genome size 2.28 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 7 July 2025
mRhiDar1.MT.20250707.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mRhiDar1.yml (view)
species: Rhinolophus darlingii
specimem: mRhiDar1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Rhinolophus_darlingii/mRhiDar1/assembly_vgp_HiC_2.0/mRhiDar1.HiC.hap1.20250707.fasta.gz
hap2: s3://genomeark/species/Rhinolophus_darlingii/mRhiDar1/assembly_vgp_HiC_2.0/mRhiDar1.HiC.hap2.20250707.fasta.gz
pretext_hap1: s3://genomeark/species/Rhinolophus_darlingii/mRhiDar1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mRhiDar1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Rhinolophus_darlingii/mRhiDar1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mRhiDar1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Rhinolophus_darlingii/mRhiDar1/assembly_vgp_HiC_2.0/evaluation/merqury/mRhiDar1_png/
pacbio_read_dir: s3://genomeark/species/Rhinolophus_darlingii/mRhiDar1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Rhinolophus_darlingii/mRhiDar1/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)
  - VGP8 HiC scaffolding workflow (v2.0)
  - VGP9 decontamination workflow (v0.7) with Kraken2 database PlusPF 2022
  - Pre-curation worklfow (v1.0beta6)
notes: This was a Hifiasm-HiC assembly of mRhiDar1 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 was generated using Arima v1 kit. The trimmed new HiC data and the old HiC data were combined and used for assembly and curation.
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.