Rhinolophus clivosus

Geoffroy'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: mRhiCli
  name: Rhinolophus clivosus
  taxon_id: 59478
  common_name: Geoffroy's horseshoe bat
  order:
    name: Chiroptera
  family:
    name: Rhinolophidae
  individuals:
    - short_name: mRhiCli1
  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) mRhiCli1 28.32 Gbp 13.47x 101.9 GiB
PacBio HiFi (.bam) mRhiCli1 112.98 Gbp 53.73x 406.6 GiB
Arima mRhiCli1 138.24 Gbp 65.74x 56.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.10 Gbp.
Last upload on 31 January 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mRhiCli1 PacBio HiFi (.fq) 28.32 Gbp 13.47x 101.9 GiB
PacBio HiFi (.bam) 112.98 Gbp 53.73x 406.6 GiB
Arima 138.24 Gbp 65.74x 56.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.10 Gbp.
Last upload on 31 January 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 10 October 2025
mRhiCli1.hap1.cur.20251010.fasta.gz (653.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 110.68 Mbp 2 119.95 Mbp
20 4 101.31 Mbp 4 111.44 Mbp
30 7 83.61 Mbp 6 103.02 Mbp
40 9 80.85 Mbp 8 100.92 Mbp
50 12 73.80 Mbp 10 93.74 Mbp
60 15 58.81 Mbp 13 80.55 Mbp
70 19 50.14 Mbp 15 68.12 Mbp
80 23 44.18 Mbp 19 61.33 Mbp
90 30 19.67 Mbp 22 53.44 Mbp
100 43 10.82 Mbp 28 19.42 Mbp
1.082x 306 2.28 Gbp 270 2.28 Gbp
NG based on genome size 2.10 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 10 October 2025
mRhiCli1.hap2.cur.20251010.fasta.gz (554.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 107.70 Mbp 2 113.13 Mbp
20 4 102.29 Mbp 4 109.50 Mbp
30 7 83.60 Mbp 6 102.32 Mbp
40 9 81.11 Mbp 8 98.73 Mbp
50 12 68.80 Mbp 11 84.67 Mbp
60 15 63.32 Mbp 13 73.64 Mbp
70 19 53.45 Mbp 16 64.03 Mbp
80 24 39.95 Mbp 20 53.70 Mbp
90 31 19.93 Mbp 24 43.33 Mbp
100 0 0
0.989x 249 2.08 Gbp 219 2.08 Gbp
NG based on genome size 2.10 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 14 February 2024
mRhiCli1.MT.20240214.fasta.gz (5.1 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mRhiCli1.yml (view)
species: Rhinolophus clivosus
specimen: mRhiCli1
projects: 
  - vgp
  - bat1k
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
primary: s3://genomeark/species/Rhinolophus_clivosus/mRhiCli1/assembly_vgp_HiC_2.0/mRhiCli1.HiC.hap1.20240214.fasta.gz
haplotigs: s3://genomeark/species/Rhinolophus_clivosus/mRhiCli1/assembly_vgp_HiC_2.0/mRhiCli1.HiC.hap2.20240214.fasta.gz
pretext: s3://genomeark/species/Rhinolophus_clivosus/mRhiCli1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mRhiCli1_hap1_s2.pretext
pretext: s3://genomeark/species/Rhinolophus_clivosus/mRhiCli1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mRhiCli1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Rhinolophus_clivosus/mRhiCli1/assembly_vgp_HiC_2.0/evaluation/merqury/mRhiCli1_png/
pacbio_read_dir: s3://genomeark/species/Rhinolophus_clivosus/mRhiCli1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Rhinolophus_clivosus/mRhiCli1/genomic_data/arima/
mito: s3://genomeark/species/Rhinolophus_clivosus/mRhiCli1/assembly_MT_rockefeller/mRhiCli1.MT.20240214.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of mRhiCli1. This hap1 assembly and hap2 assembly underwent separate HiC scaffolding with YaHS. The HiC prep kit used was Swift-IDT. The HiC reaction was using Arima kit v2.
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.