Hydrolagus colliei

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) sHydCol1 55.07 Gbp N/A 40.9 GiB
Arima sHydCol1 167.43 Gbp N/A 79.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 April 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
sHydCol1 PacBio HiFi (.fq) 55.07 Gbp N/A 40.9 GiB
Arima 167.43 Gbp N/A 79.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 April 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 25 October 2023
sHydCol1.hap1.cur.20231025.fasta.gz (307.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 21 4.26 Mbp 1 155.29 Mbp
20 55 2.64 Mbp 2 138.34 Mbp
30 105 1.89 Mbp 3 112.50 Mbp
40 173 1.38 Mbp 4 91.09 Mbp
50 264 1.04 Mbp 6 31.07 Mbp
60 388 0.77 Mbp 10 21.64 Mbp
70 560 0.53 Mbp 16 17.46 Mbp
80 821 321.87 Kbp 23 11.42 Mbp
90 1314 154.51 Kbp 55 0.94 Mbp
100 3122 10.46 Kbp 1038 10.46 Kbp
1.000x 3122 1.10 Gbp 1038 1.10 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 25 October 2023
sHydCol1.hap2.cur.20231025.fasta.gz (286.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 18 3.99 Mbp 1 156.10 Mbp
20 50 2.71 Mbp 2 137.42 Mbp
30 92 2.08 Mbp 3 111.05 Mbp
40 150 1.48 Mbp 3 111.05 Mbp
50 230 1.06 Mbp 5 42.63 Mbp
60 346 0.72 Mbp 8 23.75 Mbp
70 506 0.53 Mbp 12 18.67 Mbp
80 738 346.60 Kbp 18 14.30 Mbp
90 1143 173.46 Kbp 27 8.39 Mbp
100 2476 14.13 Kbp 528 14.13 Kbp
1.000x 2476 1.00 Gbp 528 1.00 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/sHydCol1_hap1.yml (view)
species: Hydrolagus colliei
specimen: sHydCol1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Hydrolagus_colliei/sHydCol1/assembly_vgp_HiC_2.0/sHydCol1.HiC.hap1.20230731.fasta.gz
hap2: s3://genomeark/species/Hydrolagus_colliei/sHydCol1/assembly_vgp_HiC_2.0/sHydCol1.HiC.hap2.20230731.fasta.gz
pretext_hap1: s3://genomeark/species/Hydrolagus_colliei/sHydCol1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/sHydCol1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Hydrolagus_colliei/sHydCol1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/sHydCol1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Hydrolagus_colliei/sHydCol1/assembly_vgp_HiC_2.0/evaluation/merqury/sHydCol1_png/
pacbio_read_dir: s3://genomeark/species/Hydrolagus_colliei/sHydCol1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Hydrolagus_colliei/sHydCol1/genomic_data/arima/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of sHydCol1, resulting in two complete haplotypes. This individual did not bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. MitoHiFi did not assemble a mitogenome for this sample. 
assembly_vgp_HiC_2.0/sHydCol1_hap2.yml (view)
species: Hydrolagus colliei
specimen: sHydCol1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Hydrolagus_colliei/sHydCol1/assembly_vgp_HiC_2.0/sHydCol1.HiC.hap1.20230731.fasta.gz
hap2: s3://genomeark/species/Hydrolagus_colliei/sHydCol1/assembly_vgp_HiC_2.0/sHydCol1.HiC.hap2.20230731.fasta.gz
pretext_hap1: s3://genomeark/species/Hydrolagus_colliei/sHydCol1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/sHydCol1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Hydrolagus_colliei/sHydCol1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/sHydCol1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Hydrolagus_colliei/sHydCol1/assembly_vgp_HiC_2.0/evaluation/merqury/sHydCol1_png/
pacbio_read_dir: s3://genomeark/species/Hydrolagus_colliei/sHydCol1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Hydrolagus_colliei/sHydCol1/genomic_data/arima/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of sHydCol1, resulting in two complete haplotypes. This individual did not bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. MitoHiFi did not assemble a mitogenome for this sample. 
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.