Dumetella carolinensis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bDumCar1 93.43 Gbp N/A 47.9 GiB
PacBio HiFi (.bam) bDumCar1 94.36 Gbp N/A 383.9 GiB
Arima bDumCar1 80.75 Gbp N/A 41.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 26 March 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bDumCar1 PacBio HiFi (.fq) 93.43 Gbp N/A 47.9 GiB
PacBio HiFi (.bam) 94.36 Gbp N/A 383.9 GiB
Arima 80.75 Gbp N/A 41.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 26 March 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 24 June 2024
bDumCar1.HiC.hap1.20240624.fasta.gz (353.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 66.43 Mbp 1 154.73 Mbp
20 5 50.11 Mbp 2 121.04 Mbp
30 7 43.53 Mbp 4 78.99 Mbp
40 11 28.60 Mbp 5 75.11 Mbp
50 16 22.92 Mbp 8 39.05 Mbp
60 23 16.30 Mbp 11 26.47 Mbp
70 33 11.62 Mbp 17 21.46 Mbp
80 50 4.93 Mbp 26 11.72 Mbp
90 117 0.86 Mbp 45 3.37 Mbp
100 958 12.40 Kbp 797 12.40 Kbp
1.000x 958 1.33 Gbp 797 1.33 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 24 June 2024
bDumCar1.HiC.hap2.20240624.fasta.gz (316.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 70.03 Mbp 1 153.22 Mbp
20 4 64.41 Mbp 2 118.57 Mbp
30 5 60.03 Mbp 3 116.32 Mbp
40 8 37.17 Mbp 4 78.73 Mbp
50 12 25.05 Mbp 6 52.82 Mbp
60 17 17.34 Mbp 9 32.33 Mbp
70 25 12.67 Mbp 14 21.83 Mbp
80 36 7.98 Mbp 21 12.63 Mbp
90 63 1.93 Mbp 34 5.25 Mbp
100 472 21.57 Kbp 328 21.57 Kbp
1.000x 472 1.15 Gbp 328 1.16 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/bDumCar1.yml (view)
species: Dumetella carolinensis
specimen: bDumCar1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Dumetella_carolinensis/bDumCar1/assembly_vgp_HiC_2.0/bDumCar1.HiC.hap1.20240627.fasta.gz
hap2: s3://genomeark/species/Dumetella_carolinensis/bDumCar1/assembly_vgp_HiC_2.0/bDumCar1.HiC.hap2.20240627.fasta.gz
pretext_hap1: s3://genomeark/species/Dumetella_carolinensis/bDumCar1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bDumCar1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Dumetella_carolinensis/bDumCar1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bDumCar1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Dumetella_carolinensis/bDumCar1/assembly_vgp_HiC_2.0/evaluation/merqury/bDumCar1_png/
mito: s3://genomeark/species/Dumetella_carolinensis/bDumCar1/assembly_MT_rockefeller/bDumCar1.MT.20240627.fasta.gz
pacbio_read_dir: s3://genomeark/species/Dumetella_carolinensis/bDumCar1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
pacbio_read_dir: s3://genomeark/species/Dumetella_carolinensis/bDumCar1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Dumetella_carolinensis/bDumCar1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.8+galaxy1)
  - solve (3.7)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of bDumCar1, resulting in two complete haplotypes. This sample had bionano data. The HiC prep kit used was Arima, so the HiC reads require trimming 5 bp off the 5' end. The assembly was performed on the Rockefeller University VGL instance. The VGL ID for this individual is VGL-bDumCar2.
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.