Placopecten magellanicus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 16 April 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 16 April 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 4 September 2025
xbPlaMage1.HiC.hap1.20250904.fasta.gz (304.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 12 11.21 Mbp 1 189.24 Mbp
20 28 9.32 Mbp 2 177.41 Mbp
30 49 7.30 Mbp 4 99.74 Mbp
40 73 6.45 Mbp 5 98.91 Mbp
50 103 5.00 Mbp 7 86.49 Mbp
60 143 3.77 Mbp 9 81.81 Mbp
70 194 2.83 Mbp 11 79.58 Mbp
80 266 1.91 Mbp 14 56.74 Mbp
90 384 1.03 Mbp 17 33.22 Mbp
100 1067 9.93 Kbp 530 9.93 Kbp
1.000x 1067 1.69 Gbp 530 1.69 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 4 September 2025
xbPlaMage1.HiC.hap2.20250904.fasta.gz (308.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 12 12.47 Mbp 2 161.38 Mbp
20 27 10.04 Mbp 3 119.06 Mbp
30 47 7.72 Mbp 4 103.21 Mbp
40 73 6.23 Mbp 6 96.94 Mbp
50 107 4.70 Mbp 8 86.17 Mbp
60 149 3.54 Mbp 10 81.88 Mbp
70 206 2.68 Mbp 12 74.98 Mbp
80 286 1.77 Mbp 15 59.12 Mbp
90 421 0.89 Mbp 21 3.70 Mbp
100 1460 14.64 Kbp 951 14.64 Kbp
1.000x 1460 1.77 Gbp 951 1.77 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 5 September 2025
xbPlaMage1.MT.20250905.fasta.gz (8.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/xbPlaMage1.yml (view)
species: Placopecten magellanicus
specimem: xbPlaMage1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Placopecten_magellanicus/xbPlaMage1/assembly_vgp_HiC_2.0/xbPlaMage1.HiC.hap1.20250904.fasta.gz
hap2: s3://genomeark/species/Placopecten_magellanicus/xbPlaMage1/assembly_vgp_HiC_2.0/xbPlaMage1.HiC.hap2.20250904.fasta.gz
pretext_hap1: s3://genomeark/species/Placopecten_magellanicus/xbPlaMage1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/xbPlaMage1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Placopecten_magellanicus/xbPlaMage1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/xbPlaMage1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Placopecten_magellanicus/xbPlaMage1/assembly_vgp_HiC_2.0/evaluation/merqury/xbPlaMage1_png/
pacbio_read_dir: s3://genomeark/species/Placopecten_magellanicus/xbPlaMage1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Placopecten_magellanicus/xbPlaMage1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - mitoHiFi (3.2.3.+galaxy0)
  - VGP1 genomic profiling workflow (v0.3)
  - VGP4 HiFi HiC assembly workflow (v0.3.9)
  - VGP8 HiC scaffolding workflow (v2.0) BUSCO lineage mollusca_odb10
  - VGP9 decontamination workflow (v0.7) with database PlusPF2022
  - Pre-curation worklfow (v1.0beta6)
notes: This was a Hifiasm-HiC assembly of xbPlaMage1 resulting in two haplotype assemblies. HiC data were generated using the Arima library prep kit, and require trimming the first 5 bp off from the 5' end of both read files. The restriction enzymes used were the Arima v2 kit, so the cutting sites are GATC, GANTC, CTNAG, TTAA.
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.