Pseudopleuronectes americanus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fPseAme1 29.61 Gbp N/A 18.6 GiB
Arima fPseAme1 196.60 Gbp N/A 100.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 20 July 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fPseAme1 PacBio HiFi (.fq) 29.61 Gbp N/A 18.6 GiB
Arima 196.60 Gbp N/A 100.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 20 July 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 15 August 2023
fPseAme1.HiC.hap1.20230815.fasta.gz (162.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 8 5.99 Mbp 2 27.59 Mbp
20 20 4.36 Mbp 5 26.51 Mbp
30 34 3.32 Mbp 7 25.92 Mbp
40 53 2.54 Mbp 9 25.59 Mbp
50 78 1.97 Mbp 11 23.52 Mbp
60 111 1.49 Mbp 14 22.78 Mbp
70 163 0.83 Mbp 16 21.59 Mbp
80 260 423.72 Kbp 19 19.84 Mbp
90 453 204.12 Kbp 22 16.25 Mbp
100 1363 2.97 Kbp 419 2.97 Kbp
1.000x 1363 0.57 Gbp 419 0.57 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 15 August 2023
fPseAme1.HiC.hap2.20230815.fasta.gz (160.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 7 6.93 Mbp 2 41.42 Mbp
20 17 5.12 Mbp 4 27.66 Mbp
30 30 3.69 Mbp 6 26.38 Mbp
40 47 2.75 Mbp 8 26.19 Mbp
50 70 2.09 Mbp 10 25.87 Mbp
60 102 1.50 Mbp 12 25.47 Mbp
70 149 0.98 Mbp 14 23.06 Mbp
80 227 495.70 Kbp 17 21.56 Mbp
90 417 195.01 Kbp 20 16.32 Mbp
100 1274 3.19 Kbp 337 3.19 Kbp
1.000x 1274 0.56 Gbp 337 0.56 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 15 August 2023
fPseAme1.MT.20230815.fasta.gz (5.6 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fPseAme1_hap1.yml (view)
species: Pseudopleuronectes americanus
specimen: fPseAme1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Pseudopleuronectes_americanus/fPseAme1/assembly_vgp_HiC_2.0/fPseAme1.HiC.hap1.20230815.fasta.gz
hap2: s3://genomeark/species/Pseudopleuronectes_americanus/fPseAme1/assembly_vgp_HiC_2.0/fPseAme1.HiC.hap2.20230815.fasta.gz
pretext_hap1: s3://genomeark/species/Pseudopleuronectes_americanus/fPseAme1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fPseAme1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Pseudopleuronectes_americanus/fPseAme1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fPseAme1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Pseudopleuronectes_americanus/fPseAme1/assembly_vgp_HiC_2.0/evaluation/merqury/fPseAme1_png/
mito: s3://genomeark/species/Pseudopleuronectes_americanus/fPseAme1/assembly_MT_rockefeller/fPseAme1.MT.20230815.fasta.gz
pacbio_read_dir: s3://genomeark/species/Pseudopleuronectes_americanus/fPseAme1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Pseudopleuronectes_americanus/fPseAme1/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 fPseAme1, resulting in two complete haplotypes. Sample metadata says it is a male fish, and kmer spectra indicate a homogametic specimen. 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. We are submitting both haplotypes for dual curation, and this is the ticket for hap1. 
assembly_vgp_HiC_2.0/fPseAme1_hap2.yml (view)
species: Pseudopleuronectes americanus
specimen: fPseAme1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Pseudopleuronectes_americanus/fPseAme1/assembly_vgp_HiC_2.0/fPseAme1.HiC.hap1.20230815.fasta.gz
hap2: s3://genomeark/species/Pseudopleuronectes_americanus/fPseAme1/assembly_vgp_HiC_2.0/fPseAme1.HiC.hap2.20230815.fasta.gz
pretext_hap1: s3://genomeark/species/Pseudopleuronectes_americanus/fPseAme1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fPseAme1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Pseudopleuronectes_americanus/fPseAme1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fPseAme1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Pseudopleuronectes_americanus/fPseAme1/assembly_vgp_HiC_2.0/evaluation/merqury/fPseAme1_png/
mito: s3://genomeark/species/Pseudopleuronectes_americanus/fPseAme1/assembly_MT_rockefeller/fPseAme1.MT.20230815.fasta.gz
pacbio_read_dir: s3://genomeark/species/Pseudopleuronectes_americanus/fPseAme1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Pseudopleuronectes_americanus/fPseAme1/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 fPseAme1, resulting in two complete haplotypes. Sample metadata says it is a male fish, and kmer spectra indicate a homogametic specimen. 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. We are submitting both haplotypes for dual curation, and this is the ticket for hap2. 
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.