Spirinchus thaleichthys

longfin smelt

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  name: Spirinchus thaleichthys
  individuals:
  - short_name: fSpiTha1
  short_name: fSpiTha
  taxon_id: 260508
  common_name: longfin smelt
  genome_size: 822000000
  genome_size_method: GoAT
  order:
    name: Osmeriformes
  family:
    name: Osmeridae
  project: [ vgp ]
CC BY 2.0 U.S. Bureau of Reclamation from U.S. FWS Pacific Southwest Region (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) fSpiTha1 170.47 Gbp 207.39x 381.9 GiB
PacBio HiFi (.fq) fSpiTha1 36.39 Gbp 44.27x 26.9 GiB
PacBio HiFi (.bam) fSpiTha1 36.50 Gbp 44.41x 124.0 GiB
Arima fSpiTha1 77.63 Gbp 94.44x 37.8 GiB
Illumina fSpiTha1 44.66 Gbp 54.33x 21.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.82 Gbp.
Last upload on 17 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fSpiTha1 PacBio HiFi (subreads) 170.47 Gbp 207.39x 381.9 GiB
PacBio HiFi (.fq) 36.39 Gbp 44.27x 26.9 GiB
PacBio HiFi (.bam) 36.50 Gbp 44.41x 124.0 GiB
Arima 77.63 Gbp 94.44x 37.8 GiB
Illumina 44.66 Gbp 54.33x 21.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.82 Gbp.
Last upload on 17 June 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 29 October 2025
fSpiTha1.HiC.hap1.20251029.fasta.gz (127.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 13 4.76 Mbp 11 5.88 Mbp
20 37 2.29 Mbp 29 3.71 Mbp
30 91 1.08 Mbp 58 2.19 Mbp
40 194 0.56 Mbp 109 1.17 Mbp
50 393 302.40 Kbp 205 0.62 Mbp
60 819 123.39 Kbp 398 264.17 Kbp
70 0 0
80 0 0
90 0 0
100 0 0
0.696x 2219 0.57 Gbp 1436 0.57 Gbp
NG based on genome size 0.82 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 29 October 2025
fSpiTha1.HiC.hap2.20251029.fasta.gz (133.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 11 5.43 Mbp 9 7.07 Mbp
20 33 2.80 Mbp 26 3.70 Mbp
30 78 1.24 Mbp 54 2.41 Mbp
40 167 0.71 Mbp 100 1.29 Mbp
50 330 386.22 Kbp 183 0.77 Mbp
60 638 188.10 Kbp 333 405.16 Kbp
70 1483 48.01 Kbp 779 72.04 Kbp
80 0 0
90 0 0
100 0 0
0.723x 2063 0.59 Gbp 1239 0.59 Gbp
NG based on genome size 0.82 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/fSpiTha1.yml (view)
species: Spirinchus thaleichthys
specimem: fSpiTha1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Spirinchus_thaleichthys/fSpiTha1/assembly_vgp_HiC_2.0/fSpiTha1.HiC.hap1.20251029.fasta.gz
hap2: s3://genomeark/species/Spirinchus_thaleichthys/fSpiTha1/assembly_vgp_HiC_2.0/fSpiTha1.HiC.hap2.20251029.fasta.gz
pretext_hap1: s3://genomeark/species/Spirinchus_thaleichthys/fSpiTha1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fSpiTha1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Spirinchus_thaleichthys/fSpiTha1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fSpiTha1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Spirinchus_thaleichthys/fSpiTha1/assembly_vgp_HiC_2.0/evaluation/merqury/fSpiTha1_png/
pacbio_read_dir: s3://genomeark/species/Spirinchus_thaleichthys/fSpiTha1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Spirinchus_thaleichthys/fSpiTha1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - 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 fSpiTha1 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. MitoHiFi failed (workflow v0.2.2), probably due to too few reads (n=6).
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.