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_curated from 18 December 2025
fPseAme1.hap1.cur.20251218.fasta.gz (162.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 8 5.99 Mbp 2 28.27 Mbp
20 18 4.64 Mbp 5 26.67 Mbp
30 32 3.69 Mbp 7 26.39 Mbp
40 49 2.97 Mbp 9 26.11 Mbp
50 73 2.17 Mbp 11 25.87 Mbp
60 105 1.45 Mbp 13 23.39 Mbp
70 156 0.87 Mbp 16 21.80 Mbp
80 249 441.74 Kbp 19 20.05 Mbp
90 443 195.77 Kbp 22 16.53 Mbp
100 1324 10.07 Kbp 344 10.07 Kbp
1.000x 1324 0.57 Gbp 344 0.57 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 18 December 2025
fPseAme1.hap2.cur.20251218.fasta.gz (160.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 8 6.22 Mbp 2 27.90 Mbp
20 19 4.65 Mbp 5 26.58 Mbp
30 33 3.27 Mbp 7 26.42 Mbp
40 53 2.52 Mbp 9 25.74 Mbp
50 79 1.91 Mbp 11 25.42 Mbp
60 112 1.50 Mbp 13 23.05 Mbp
70 160 0.92 Mbp 16 21.59 Mbp
80 243 460.95 Kbp 19 19.84 Mbp
90 430 199.79 Kbp 21 18.91 Mbp
100 1230 10.06 Kbp 284 10.06 Kbp
1.000x 1230 0.56 Gbp 284 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.