Rhinopoma cystops

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mRhiCys1 29.89 Gbp N/A 106.6 GiB
PacBio HiFi (.bam) mRhiCys1 125.02 Gbp N/A 445.8 GiB
Arima mRhiCys1 171.90 Gbp N/A 72.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 23 November 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mRhiCys1 PacBio HiFi (.fq) 29.89 Gbp N/A 106.6 GiB
PacBio HiFi (.bam) 125.02 Gbp N/A 445.8 GiB
Arima 171.90 Gbp N/A 72.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 23 November 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 4 December 2023
mRhiCys1.HiC.hap1.20231204.fasta.gz (803.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 75.81 Mbp 2 175.78 Mbp
20 8 60.08 Mbp 4 173.05 Mbp
30 14 50.50 Mbp 6 154.77 Mbp
40 22 37.08 Mbp 8 130.66 Mbp
50 31 31.80 Mbp 10 125.81 Mbp
60 42 26.65 Mbp 13 113.78 Mbp
70 55 17.99 Mbp 16 86.40 Mbp
80 80 9.39 Mbp 21 46.40 Mbp
90 137 3.64 Mbp 59 3.98 Mbp
100 640 14.34 Kbp 552 14.34 Kbp
1.000x 640 3.18 Gbp 552 3.18 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 4 December 2023
mRhiCys1.HiC.hap2.20231204.fasta.gz (741.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 95.23 Mbp 2 233.91 Mbp
20 7 70.62 Mbp 3 180.11 Mbp
30 11 59.46 Mbp 5 174.25 Mbp
40 17 43.62 Mbp 6 170.56 Mbp
50 25 32.76 Mbp 8 145.44 Mbp
60 35 24.09 Mbp 10 123.23 Mbp
70 49 15.71 Mbp 14 72.75 Mbp
80 74 8.52 Mbp 19 43.62 Mbp
90 129 3.28 Mbp 52 3.83 Mbp
100 577 13.17 Kbp 488 13.17 Kbp
1.000x 577 2.87 Gbp 488 2.87 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 4 December 2023
mRhiCys1.MT.20231204.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mRhiCys1.yml (view)
species: Rhinopoma cystops
specimen: mRhiCys1
projects: 
  - vgp
  - bat1k
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
primary: s3://genomeark/species/Rhinopoma_cystops/mRhiCys1/assembly_vgp_HiC_2.0/mRhiCys1.HiC.hap1.20231204.fasta.gz
haplotigs: s3://genomeark/species/Rhinopoma_cystops/mRhiCys1/assembly_vgp_HiC_2.0/mRhiCys1.HiC.hap2.20231204.fasta.gz
pretext: s3://genomeark/species/Rhinopoma_cystops/mRhiCys1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mRhiCys1_hap1_s2.pretext
pretext: s3://genomeark/species/Rhinopoma_cystops/mRhiCys1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mRhiCys1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Rhinopoma_cystops/mRhiCys1/assembly_vgp_HiC_2.0/evaluation/merqury/mRhiCys1_png/
pacbio_read_dir: s3://genomeark/species/Rhinopoma_cystops/mRhiCys1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Rhinopoma_cystops/mRhiCys1/genomic_data/arima/
mito: s3://genomeark/species/Rhinopoma_cystops/mRhiCys1/assembly_MT_rockefeller/mRhiCys1.MT.20231204.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of mRhiCys1. 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.