Stylephorus chordatus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fStyCho2 42.71 Gbp N/A 19.3 GiB
PacBio HiFi (.bam) fStyCho2 44.89 Gbp N/A 148.8 GiB
Arima fStyCho2 50.55 Gbp N/A 26.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 27 February 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fStyCho2 PacBio HiFi (.fq) 42.71 Gbp N/A 19.3 GiB
PacBio HiFi (.bam) 44.89 Gbp N/A 148.8 GiB
Arima 50.55 Gbp N/A 26.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 27 February 2025.
Assemblies
Individual 2 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 29 October 2025
fStyCho2.HiC.hap1.20251029.fasta.gz (280.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 30 2.84 Mbp 1 231.77 Mbp
20 80 1.98 Mbp 2 182.44 Mbp
30 150 1.42 Mbp 2 182.44 Mbp
40 246 1.05 Mbp 3 165.56 Mbp
50 374 0.82 Mbp 4 88.77 Mbp
60 542 0.59 Mbp 5 79.70 Mbp
70 781 394.24 Kbp 7 43.64 Mbp
80 1175 218.47 Kbp 10 36.20 Mbp
90 2030 83.18 Kbp 51 0.52 Mbp
100 6804 3.29 Kbp 4057 3.29 Kbp
1.000x 6804 1.17 Gbp 4057 1.17 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 29 October 2025
fStyCho2.HiC.hap2.20251029.fasta.gz (275.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 26 3.22 Mbp 1 183.67 Mbp
20 70 2.21 Mbp 2 169.82 Mbp
30 132 1.57 Mbp 2 169.82 Mbp
40 218 1.18 Mbp 3 130.12 Mbp
50 334 0.84 Mbp 4 114.56 Mbp
60 493 0.62 Mbp 5 93.36 Mbp
70 720 419.16 Kbp 7 50.99 Mbp
80 1073 252.02 Kbp 10 39.13 Mbp
90 1743 113.23 Kbp 25 1.09 Mbp
100 4781 3.81 Kbp 2008 3.81 Kbp
1.000x 4781 1.15 Gbp 2008 1.15 Gbp
NG based on genome size .
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 29 October 2025
fStyCho2.MT.20251029.fasta.gz (5.5 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fStyCho2.yml (view)
species: Stylephorus chordatus
specimem: fStyCho2
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Stylephorus_chordatus/fStyCho2/assembly_vgp_HiC_2.0/fStyCho2.HiC.hap1.20251029.fasta.gz
hap2: s3://genomeark/species/Stylephorus_chordatus/fStyCho2/assembly_vgp_HiC_2.0/fStyCho2.HiC.hap2.20251029.fasta.gz
pretext_hap1: s3://genomeark/species/Stylephorus_chordatus/fStyCho2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fStyCho2_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Stylephorus_chordatus/fStyCho2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fStyCho2_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Stylephorus_chordatus/fStyCho2/assembly_vgp_HiC_2.0/evaluation/merqury/fStyCho2_png/
pacbio_read_dir: s3://genomeark/species/Stylephorus_chordatus/fStyCho2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Stylephorus_chordatus/fStyCho2/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.5)
  - VGP4 HiFi HiC assembly workflow (v0.4)
  - VGP8 HiC scaffolding workflow (v3.1) with mapq=10
  - VGP9 decontamination workflow (v1.1) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of fStyCho2 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.