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_curated from 12 May 2026
xbPlaMage1.hap1.cur.20260512.fasta.gz (364.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 11 12.47 Mbp 2 104.45 Mbp
20 27 10.13 Mbp 4 99.74 Mbp
30 46 7.95 Mbp 5 95.61 Mbp
40 71 6.28 Mbp 7 90.43 Mbp
50 102 4.74 Mbp 9 86.17 Mbp
60 141 3.87 Mbp 11 84.43 Mbp
70 193 2.90 Mbp 13 81.81 Mbp
80 261 2.01 Mbp 16 72.58 Mbp
90 369 1.22 Mbp 18 59.89 Mbp
100 998 12.74 Kbp 464 12.74 Kbp
1.000x 998 1.71 Gbp 464 1.71 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 12 May 2026
xbPlaMage1.hap2.cur.20260512.fasta.gz (363.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 12 11.71 Mbp 2 103.21 Mbp
20 29 9.16 Mbp 4 96.94 Mbp
30 51 7.30 Mbp 6 86.00 Mbp
40 76 6.22 Mbp 8 84.71 Mbp
50 109 4.66 Mbp 10 84.55 Mbp
60 152 3.45 Mbp 12 81.88 Mbp
70 212 2.52 Mbp 14 78.91 Mbp
80 297 1.64 Mbp 16 72.04 Mbp
90 448 0.79 Mbp 19 54.64 Mbp
100 1490 14.64 Kbp 932 14.64 Kbp
1.000x 1490 1.74 Gbp 932 1.74 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.