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_vgp_HiC_2.0 from 7 July 2025
mRhiDar1.HiC.hap1.20250707.fasta.gz (548.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 102.60 Mbp 2 110.95 Mbp
20 5 95.38 Mbp 4 110.18 Mbp
30 7 88.92 Mbp 6 101.67 Mbp
40 11 64.25 Mbp 9 92.58 Mbp
50 14 58.16 Mbp 11 88.13 Mbp
60 19 52.14 Mbp 14 69.17 Mbp
70 23 43.15 Mbp 18 57.83 Mbp
80 30 24.23 Mbp 22 45.49 Mbp
90 0 0
100 0 0
0.899x 380 2.05 Gbp 337 2.05 Gbp
NG based on genome size 2.28 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 7 July 2025
mRhiDar1.HiC.hap2.20250707.fasta.gz (585.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 100.93 Mbp 1 283.04 Mbp
20 5 96.10 Mbp 3 159.23 Mbp
30 7 92.90 Mbp 4 128.38 Mbp
40 10 77.76 Mbp 6 110.68 Mbp
50 13 68.78 Mbp 8 107.17 Mbp
60 17 56.29 Mbp 10 92.90 Mbp
70 21 46.79 Mbp 13 77.76 Mbp
80 27 31.05 Mbp 16 64.91 Mbp
90 38 9.62 Mbp 20 50.23 Mbp
100 0 0
0.995x 941 2.27 Gbp 836 2.27 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.