Fundulus diaphanus

banded killifish

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  name: Fundulus diaphanus
  individuals:
  - short_name: fFunDia1
  short_name: fFunDia
  taxon_id: 54267
  common_name: banded killifish
  genome_size: 1515000000
  genome_size_method: GoAT
  order:
    name: Cyprinodontiformes
  family:
    name: Fundulidae
  project: [ vgp ]
CC BY 2.0 Smithsonian Environmental Research Center (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fFunDia1 48.47 Gbp 31.99x 32.9 GiB
Bionano fFunDia1 N/A 613.16x 1.6 GiB
Arima fFunDia1 185.87 Gbp 122.69x 88.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.52 Gbp.
Last upload on 9 May 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fFunDia1 PacBio HiFi (.fq) 48.47 Gbp 31.99x 32.9 GiB
Bionano N/A 613.16x 1.6 GiB
Arima 185.87 Gbp 122.69x 88.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.52 Gbp.
Last upload on 9 May 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 26 January 2024
fFunDia1.hap1.cur.20240126.fasta.gz (380.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 25.28 Mbp 3 62.97 Mbp
20 11 23.28 Mbp 5 62.36 Mbp
30 19 17.96 Mbp 8 59.47 Mbp
40 29 12.65 Mbp 10 58.15 Mbp
50 43 9.44 Mbp 13 57.09 Mbp
60 64 6.18 Mbp 16 54.21 Mbp
70 96 3.77 Mbp 19 49.44 Mbp
80 154 1.83 Mbp 22 46.11 Mbp
90 0 0
100 0 0
0.890x 623 1.35 Gbp 330 1.35 Gbp
NG based on genome size 1.52 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 26 January 2024
fFunDia1.hap2.cur.20240126.fasta.gz (375.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 21.76 Mbp 3 63.52 Mbp
20 15 15.88 Mbp 5 61.47 Mbp
30 26 12.33 Mbp 8 58.20 Mbp
40 39 9.72 Mbp 10 57.41 Mbp
50 59 6.46 Mbp 13 54.96 Mbp
60 87 4.29 Mbp 16 52.78 Mbp
70 130 2.66 Mbp 19 49.99 Mbp
80 216 1.28 Mbp 22 45.79 Mbp
90 0 0
100 0 0
0.874x 569 1.32 Gbp 196 1.33 Gbp
NG based on genome size 1.52 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 9 May 2023
fFunDia1.MT.20230509.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fFunDia1_hap1.yml (view)
species: Fundulus diaphanus
specimen: fFunDia1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Fundulus_diaphanus/fFunDia1/assembly_vgp_HiC_2.0/fFunDia1.HiC.hap1.20230523.fasta.gz
hap2: s3://genomeark/species/Fundulus_diaphanus/fFunDia1/assembly_vgp_HiC_2.0/fFunDia1.HiC.hap2.20230523.fasta.gz
pretext_hap1: s3://genomeark/species/Fundulus_diaphanus/fFunDia1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fFunDia1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Fundulus_diaphanus/fFunDia1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fFunDia1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Fundulus_diaphanus/fFunDia1/assembly_vgp_HiC_2.0/evaluation/merqury/fFunDia1_png/
mito: s3://genomeark/species/Fundulus_diaphanus/fFunDia1/assembly_MT_rockefeller/fFunDia1.MT.20230509.fasta.gz
pacbio_read_dir: s3://genomeark/species/Fundulus_diaphanus/fFunDia1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Fundulus_diaphanus/fFunDia1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Fundulus_diaphanus/fFunDia1/genomic_data/arima/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - solve (3.7)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of fFunDia1, resulting in two complete haplotypes. This individual did have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The kmer spectra indicate a homogametic specimen. I am submitting both hap1 & hap2 for dual curation. This is the curation ticket for hap1. 
assembly_vgp_HiC_2.0/fFunDia1_hap2.yml (view)
species: Fundulus diaphanus
specimen: fFunDia1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Fundulus_diaphanus/fFunDia1/assembly_vgp_HiC_2.0/fFunDia1.HiC.hap1.20230523.fasta.gz
hap2: s3://genomeark/species/Fundulus_diaphanus/fFunDia1/assembly_vgp_HiC_2.0/fFunDia1.HiC.hap2.20230523.fasta.gz
pretext_hap1: s3://genomeark/species/Fundulus_diaphanus/fFunDia1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fFunDia1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Fundulus_diaphanus/fFunDia1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fFunDia1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Fundulus_diaphanus/fFunDia1/assembly_vgp_HiC_2.0/evaluation/merqury/fFunDia1_png/
mito: s3://genomeark/species/Fundulus_diaphanus/fFunDia1/assembly_MT_rockefeller/fFunDia1.MT.20230509.fasta.gz
pacbio_read_dir: s3://genomeark/species/Fundulus_diaphanus/fFunDia1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Fundulus_diaphanus/fFunDia1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Fundulus_diaphanus/fFunDia1/genomic_data/arima/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - solve (3.7)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of fFunDia1, resulting in two complete haplotypes. This individual did have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The kmer spectra indicate a homogametic specimen. I am submitting both hap1 & hap2 for dual curation. This is the curation ticket for hap2. 
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.