Psilogobius mainlandi

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fPsiMai1 117.93 Gbp N/A 52.7 GiB
PacBio HiFi (.bam) fPsiMai1 120.50 Gbp N/A 391.6 GiB
Arima fPsiMai1 106.17 Gbp N/A 55.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 10 June 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fPsiMai1 PacBio HiFi (.fq) 117.93 Gbp N/A 52.7 GiB
PacBio HiFi (.bam) 120.50 Gbp N/A 391.6 GiB
Arima 106.17 Gbp N/A 55.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 10 June 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 25 September 2025
fPsiMai1.HiC.hap1.20250925.fasta.gz (352.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 55.74 Mbp 1 252.94 Mbp
20 5 50.90 Mbp 2 119.01 Mbp
30 8 46.87 Mbp 3 69.30 Mbp
40 11 45.22 Mbp 5 63.00 Mbp
50 15 32.90 Mbp 7 62.28 Mbp
60 20 21.16 Mbp 10 58.73 Mbp
70 27 17.24 Mbp 12 56.28 Mbp
80 37 12.06 Mbp 15 52.95 Mbp
90 51 6.35 Mbp 17 44.05 Mbp
100 330 13.49 Kbp 259 13.49 Kbp
1.000x 330 1.38 Gbp 259 1.38 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 25 September 2025
fPsiMai1.HiC.hap2.20250925.fasta.gz (351.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 47.92 Mbp 2 109.91 Mbp
20 6 46.44 Mbp 3 93.70 Mbp
30 9 42.58 Mbp 4 82.62 Mbp
40 13 36.69 Mbp 7 62.31 Mbp
50 17 27.80 Mbp 9 60.86 Mbp
60 22 23.80 Mbp 11 59.14 Mbp
70 29 18.28 Mbp 14 56.67 Mbp
80 37 13.80 Mbp 16 52.85 Mbp
90 50 7.22 Mbp 19 45.16 Mbp
100 238 12.92 Kbp 162 12.92 Kbp
1.000x 238 1.37 Gbp 162 1.37 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 12 September 2025
fPsiMai1.MT.20250912.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fPsiMai1.yml (view)
species: Psilogobius mainlandi
specimem: fPsiMai1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Psilogobius_mainlandi/fPsiMai1/assembly_vgp_HiC_2.0/fPsiMai1.HiC.hap1.20250925.fasta.gz
hap2: s3://genomeark/species/Psilogobius_mainlandi/fPsiMai1/assembly_vgp_HiC_2.0/fPsiMai1.HiC.hap2.20250925.fasta.gz
pretext_hap1: s3://genomeark/species/Psilogobius_mainlandi/fPsiMai1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fPsiMai1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Psilogobius_mainlandi/fPsiMai1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fPsiMai1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Psilogobius_mainlandi/fPsiMai1/assembly_vgp_HiC_2.0/evaluation/merqury/fPsiMai1_png/
pacbio_read_dir: s3://genomeark/species/Psilogobius_mainlandi/fPsiMai1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Psilogobius_mainlandi/fPsiMai1/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 (v0.5.5+galaxy0) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of fPsiMai1 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.