Rhinolophus darlingi

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mRhiDar1 103.79 Gbp N/A 84.6 GiB
PacBio HiFi (.bam) mRhiDar1 104.60 Gbp N/A 366.4 GiB
Arima mRhiDar1 156.36 Gbp N/A 68.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 May 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mRhiDar1 PacBio HiFi (.fq) 103.79 Gbp N/A 84.6 GiB
PacBio HiFi (.bam) 104.60 Gbp N/A 366.4 GiB
Arima 156.36 Gbp N/A 68.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 May 2026.
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 6 101.67 Mbp
40 10 67.15 Mbp 9 95.20 Mbp
50 14 58.16 Mbp 11 88.92 Mbp
60 18 52.72 Mbp 13 77.81 Mbp
70 22 45.67 Mbp 17 64.25 Mbp
80 27 38.48 Mbp 20 55.62 Mbp
90 34 19.35 Mbp 25 39.80 Mbp
100 281 19.18 Kbp 222 19.18 Kbp
1.000x 281 2.18 Gbp 222 2.18 Gbp
NG based on genome size .
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 2 110.68 Mbp
20 5 96.10 Mbp 4 107.17 Mbp
30 7 92.90 Mbp 6 101.02 Mbp
40 9 79.98 Mbp 9 92.90 Mbp
50 12 72.05 Mbp 11 87.75 Mbp
60 15 64.91 Mbp 14 68.70 Mbp
70 19 48.54 Mbp 17 60.08 Mbp
80 24 39.15 Mbp 21 51.46 Mbp
90 34 9.62 Mbp 26 27.64 Mbp
100 926 206 bp 822 18.08 Kbp
1.000x 926 2.13 Gbp 822 2.13 Gbp
NG based on genome size .
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.