Phyllops falcatus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mPhyFal1 110.69 Gbp N/A 91.1 GiB
PacBio HiFi (.bam) mPhyFal1 108.34 Gbp N/A 383.6 GiB
Arima mPhyFal1 167.63 Gbp N/A 92.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 30 March 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mPhyFal1 PacBio HiFi (.fq) 110.69 Gbp N/A 91.1 GiB
PacBio HiFi (.bam) 108.34 Gbp N/A 383.6 GiB
Arima 167.63 Gbp N/A 92.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 30 March 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 19 May 2026
mPhyFal1.HiC.hap1.20260519.fasta.gz (582.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 162.37 Mbp 1 249.58 Mbp
20 3 143.69 Mbp 2 224.78 Mbp
30 5 128.46 Mbp 4 186.29 Mbp
40 7 111.25 Mbp 5 178.89 Mbp
50 9 87.21 Mbp 6 164.20 Mbp
60 12 62.82 Mbp 8 149.75 Mbp
70 17 52.23 Mbp 9 149.35 Mbp
80 22 35.50 Mbp 11 120.10 Mbp
90 29 20.78 Mbp 13 96.38 Mbp
100 244 16.71 Kbp 212 16.71 Kbp
1.000x 244 2.29 Gbp 212 2.29 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 19 May 2026
mPhyFal1.HiC.hap2.20260519.fasta.gz (552.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 128.73 Mbp 1 298.30 Mbp
20 4 128.19 Mbp 2 244.35 Mbp
30 5 114.90 Mbp 3 222.46 Mbp
40 8 89.38 Mbp 4 197.11 Mbp
50 10 71.74 Mbp 5 165.09 Mbp
60 14 56.59 Mbp 6 158.51 Mbp
70 18 36.31 Mbp 8 140.73 Mbp
80 24 30.60 Mbp 9 128.19 Mbp
90 32 22.24 Mbp 11 95.64 Mbp
100 168 16.71 Kbp 122 16.71 Kbp
1.000x 168 2.12 Gbp 122 2.12 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 19 May 2026
mPhyFal1.MT.20260519.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mPhyFal1.yml (view)
species: Phyllops falcatus
specimen: mPhyFal1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Phyllops_falcatus/mPhyFal1/assembly_vgp_HiC_2.0/mPhyFal1.HiC.hap1.20260519.fasta.gz
hap2: s3://genomeark/species/Phyllops_falcatus/mPhyFal1/assembly_vgp_HiC_2.0/mPhyFal1.HiC.hap2.20260519.fasta.gz
pretext_hap1: s3://genomeark/species/Phyllops_falcatus/mPhyFal1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mPhyFal1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Phyllops_falcatus/mPhyFal1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mPhyFal1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Phyllops_falcatus/mPhyFal1/assembly_vgp_HiC_2.0/evaluation/merqury/mPhyFal1_png/
pacbio_read_dir: s3://genomeark/species/Phyllops_falcatus/mPhyFal1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Phyllops_falcatus/mPhyFal1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy3)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.9)
  - VGP4 HiFi HiC assembly workflow (v0.6)
  - VGP8 HiC scaffolding workflow (v3.5) with mapq=10
  - VGP9 decontamination workflow (v1.3)
  - Pre-curation workflow (v2.4) with mapq=10, keep HiC duplicates and default high-resolution map
notes: This was a Hifiasm-HiC assembly of mPhyFal1 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.