Hypomesus transpacificus

delta smelt

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  name: Hypomesus transpacificus
  individuals:
  - short_name: fHypTra1
  short_name: fHypTra
  taxon_id: 137520
  common_name: delta smelt
  genome_size: 724000000
  genome_size_method: GoAT
  order:
    name: Osmeriformes
  family:
    name: Osmeridae
  project: [ vgp ]
Public Domain (Piqsels)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) fHypTra1 672.60 Gbp 929.01x 1.2 TiB
PacBio HiFi (.fq, Q≥20) fHypTra1 11.19 Gbp 15.45x 7.7 GiB
PacBio HiFi (.fq) fHypTra1 49.25 Gbp 68.03x 34.7 GiB
PacBio HiFi (.bam) fHypTra1 24.52 Gbp 33.87x 16.5 GiB
10x fHypTra1 130.86 Gbp 180.74x 62.9 GiB
Bionano fHypTra1 N/A 763.15x 780.3 MiB
Arima fHypTra1 154.91 Gbp 213.97x 76.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.72 Gbp.
Last upload on 6 April 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fHypTra1 PacBio HiFi (subreads) 672.60 Gbp 929.01x 1.2 TiB
PacBio HiFi (.fq, Q≥20) 11.19 Gbp 15.45x 7.7 GiB
PacBio HiFi (.fq) 49.25 Gbp 68.03x 34.7 GiB
PacBio HiFi (.bam) 24.52 Gbp 33.87x 16.5 GiB
10x 130.86 Gbp 180.74x 62.9 GiB
Bionano N/A 763.15x 780.3 MiB
Arima 154.91 Gbp 213.97x 76.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.72 Gbp.
Last upload on 6 April 2026.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 17 October 2025
fHypTra1.pri.cur.20251017.fasta.gz (137.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 15 3.16 Mbp 3 22.94 Mbp
20 48 1.39 Mbp 7 20.23 Mbp
30 127 0.69 Mbp 11 17.74 Mbp
40 274 371.59 Kbp 15 15.16 Mbp
50 549 191.76 Kbp 20 12.90 Mbp
60 1102 91.36 Kbp 27 8.32 Mbp
70 2611 22.14 Kbp 436 27.70 Kbp
80 0 0
90 0 0
100 0 0
0.709x 2972 0.51 Gbp 805 0.51 Gbp
NG based on genome size 0.72 Gbp.
Individual 1 Alternate Assembly
No assembly available.


Contigs Scaffolds
NG LG Len LG Len
10 - - - -
20 - - - -
30 - - - -
40 - - - -
50 - - - -
60 - - - -
70 - - - -
80 - - - -
90 - - - -
100 - - - -
0.000x - 0.0 Mbp - 0.0 Mbp
Assembly Metadata
assembly_vgp_standard_2.0/fHypTra1.yaml (view)
species: Hypomesus transpacificus
specimen: fHypTra1
projects: 
  - vgp
data_location: S3
release_to: S3
primary: s3://genomeark/species/Hypomesus_transpacificus/fHypTra1/assembly_vgp_standard_2.0/fHypTra1.standard.pri.20240515.fasta.gz
haplotigs: s3://genomeark/species/Hypomesus_transpacificus/fHypTra1/assembly_vgp_standard_2.0/fHypTra1.standard.alt.20240515.fasta.gz
pretext: s3://genomeark/species/Hypomesus_transpacificus/fHypTra1/assembly_vgp_standard_2.0/evaluation/pri/pretext/fHypTra1_pri__s2.heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Hypomesus_transpacificus/fHypTra1/assembly_vgp_standard_2.0/evaluation/merqury/fHypTra1_png/
pacbio_read_dir: s3://genomeark/species/Hypomesus_transpacificus/fHypTra1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Hypomesus_transpacificus/fHypTra1/genomic_data/arima/
pipeline:
  - hifiasm (0.18.8+galaxy1)
  - purge_dups (1.2.6+galaxy0)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a primary/alternate assembly of fHypTra1. This individual did not have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2, and the library prep kit was Swift-IDT. The HiFi k-mers were not informative for merqury, so illumina k-mers were used. 
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.