Polyacanthonotus merretti

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fPolMer1 78.30 Gbp N/A 36.8 GiB
PacBio HiFi (.bam) fPolMer1 80.97 Gbp N/A 268.7 GiB
Arima fPolMer1 82.96 Gbp N/A 45.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 26 March 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fPolMer1 PacBio HiFi (.fq) 78.30 Gbp N/A 36.8 GiB
PacBio HiFi (.bam) 80.97 Gbp N/A 268.7 GiB
Arima 82.96 Gbp N/A 45.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 26 March 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 20 April 2026
fPolMer1.HiC.hap1.20260420.fasta.gz (297.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 71.12 Mbp 1 150.98 Mbp
20 3 68.79 Mbp 2 110.04 Mbp
30 6 46.90 Mbp 3 104.56 Mbp
40 8 37.51 Mbp 4 104.50 Mbp
50 11 35.29 Mbp 6 97.53 Mbp
60 15 30.86 Mbp 7 91.89 Mbp
70 19 24.35 Mbp 8 82.96 Mbp
80 26 9.28 Mbp 9 78.05 Mbp
90 50 2.66 Mbp 11 64.91 Mbp
100 385 8.49 Kbp 150 8.49 Kbp
1.000x 385 1.15 Gbp 150 1.15 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 20 April 2026
fPolMer1.HiC.hap2.20260420.fasta.gz (320.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 89.73 Mbp 1 151.41 Mbp
20 3 70.93 Mbp 2 111.62 Mbp
30 5 47.48 Mbp 3 110.00 Mbp
40 9 39.16 Mbp 5 101.72 Mbp
50 12 35.66 Mbp 6 99.56 Mbp
60 15 30.94 Mbp 7 98.35 Mbp
70 21 19.60 Mbp 8 92.82 Mbp
80 29 11.82 Mbp 10 77.55 Mbp
90 54 2.25 Mbp 12 64.91 Mbp
100 332 7.05 Kbp 90 7.05 Kbp
1.000x 332 1.23 Gbp 90 1.23 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 20 April 2026
fPolMer1.MT.20260420.fasta.gz (5.5 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fPolMer1.yml (view)
species: Polyacanthonotus merretti
specimen: fPolMer1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Polyacanthonotus_merretti/fPolMer1/assembly_vgp_HiC_2.0/fPolMer1.HiC.hap1.20260420.fasta.gz
hap2: s3://genomeark/species/Polyacanthonotus_merretti/fPolMer1/assembly_vgp_HiC_2.0/fPolMer1.HiC.hap2.20260420.fasta.gz
pretext_hap1: s3://genomeark/species/Polyacanthonotus_merretti/fPolMer1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fPolMer1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Polyacanthonotus_merretti/fPolMer1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fPolMer1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Polyacanthonotus_merretti/fPolMer1/assembly_vgp_HiC_2.0/evaluation/merqury/fPolMer1_png/
pacbio_read_dir: s3://genomeark/species/Polyacanthonotus_merretti/fPolMer1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Polyacanthonotus_merretti/fPolMer1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy3)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v20260331 update)
  - VGP4 HiFi HiC assembly workflow (v0.6)
  - VGP8 HiC scaffolding workflow (v3.5) with mapq=10
  - VGP9 decontamination workflow (v1.3)
  - Pre-curation workflow (v20260330) with mapq=10, keep HiC duplicates and generate high-resolution map
notes: This was a Hifiasm-HiC assembly of fPolMer1 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.