Lepisosteus platostomus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fLepPlt1 113.40 Gbp N/A 50.9 GiB
PacBio HiFi (.bam) fLepPlt1 117.96 Gbp N/A 383.8 GiB
Arima fLepPlt1 75.72 Gbp N/A 41.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 July 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fLepPlt1 PacBio HiFi (.fq) 113.40 Gbp N/A 50.9 GiB
PacBio HiFi (.bam) 117.96 Gbp N/A 383.8 GiB
Arima 75.72 Gbp N/A 41.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 July 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 2 October 2025
fLepPlt1.HiC.hap1.20251002.fasta.gz (279.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 55.75 Mbp 2 81.10 Mbp
20 5 41.60 Mbp 3 76.45 Mbp
30 8 35.22 Mbp 5 65.81 Mbp
40 11 33.54 Mbp 7 61.98 Mbp
50 15 27.27 Mbp 9 52.94 Mbp
60 19 24.14 Mbp 11 44.78 Mbp
70 25 18.42 Mbp 14 40.59 Mbp
80 31 15.78 Mbp 17 24.14 Mbp
90 42 6.54 Mbp 23 18.06 Mbp
100 316 12.10 Kbp 275 12.10 Kbp
1.000x 316 1.15 Gbp 275 1.15 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 2 October 2025
fLepPlt1.HiC.hap2.20251002.fasta.gz (293.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 53.90 Mbp 2 82.19 Mbp
20 5 42.84 Mbp 4 77.34 Mbp
30 8 34.91 Mbp 5 69.26 Mbp
40 12 28.83 Mbp 7 63.34 Mbp
50 17 26.24 Mbp 9 55.82 Mbp
60 22 22.31 Mbp 12 44.42 Mbp
70 28 18.27 Mbp 15 26.87 Mbp
80 35 16.54 Mbp 21 17.90 Mbp
90 46 4.66 Mbp 29 12.59 Mbp
100 265 32.23 Kbp 235 32.23 Kbp
1.000x 265 1.24 Gbp 235 1.24 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 2 October 2025
fLepPlt1.MT.20251002.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fLepPlt1.yml (view)
species: Lepisosteus platostomus
specimem: fLepPlt1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Lepisosteus_platostomus/fLepPlt1/assembly_vgp_HiC_2.0/fLepPlt1.HiC.hap1.20251002.fasta.gz
hap2: s3://genomeark/species/Lepisosteus_platostomus/fLepPlt1/assembly_vgp_HiC_2.0/fLepPlt1.HiC.hap2.20251002.fasta.gz
pretext_hap1: s3://genomeark/species/Lepisosteus_platostomus/fLepPlt1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fLepPlt1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Lepisosteus_platostomus/fLepPlt1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fLepPlt1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Lepisosteus_platostomus/fLepPlt1/assembly_vgp_HiC_2.0/evaluation/merqury/fLepPlt1_png/
pacbio_read_dir: s3://genomeark/species/Lepisosteus_platostomus/fLepPlt1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Lepisosteus_platostomus/fLepPlt1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.12)
  - VGP8 HiC scaffolding workflow (v2.2) with mapq=10
  - VGP9 decontamination workflow unpublished using FCS (0.5.5+galaxy0) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of fLepPlt1 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.