Leptodactylus fuscus

rufous frog

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  name: Leptodactylus fuscus
  individuals:
  - short_name: aLepFus1
  short_name: aLepFus
  taxon_id: 238119
  common_name: rufous frog
  genome_size: 2592000000
  genome_size_method: GoAT
  order:
    name: Anura
  family:
    name: Leptodactylidae
  project: [ vgp ]
CC BY-SA 2.5 Esteban Alzate (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) aLepFus1 85.82 Gbp 33.11x 62.9 GiB
Arima aLepFus1 237.77 Gbp 91.73x 115.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.59 Gbp.
Last upload on 29 March 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aLepFus1 PacBio HiFi (.fq) 85.82 Gbp 33.11x 62.9 GiB
Arima 237.77 Gbp 91.73x 115.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.59 Gbp.
Last upload on 29 March 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 18 July 2023
aLepFus1.hap1.cur.20230718.fasta.gz (576.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 13 14.21 Mbp 1 373.86 Mbp
20 33 11.34 Mbp 2 290.10 Mbp
30 59 8.73 Mbp 3 258.30 Mbp
40 95 6.26 Mbp 4 228.30 Mbp
50 142 4.74 Mbp 5 228.26 Mbp
60 213 2.91 Mbp 6 192.84 Mbp
70 338 1.44 Mbp 8 99.29 Mbp
80 684 366.04 Kbp 11 88.79 Mbp
90 0 0
100 0 0
0.886x 3239 2.30 Gbp 2266 2.31 Gbp
NG based on genome size 2.59 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 18 July 2023
aLepFus1.hap2.cur.20230718.fasta.gz (560.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 15 15.34 Mbp 1 371.06 Mbp
20 34 12.09 Mbp 2 285.84 Mbp
30 60 8.04 Mbp 3 249.12 Mbp
40 99 5.74 Mbp 4 226.02 Mbp
50 151 4.05 Mbp 5 222.31 Mbp
60 233 2.44 Mbp 7 156.14 Mbp
70 389 1.11 Mbp 9 91.39 Mbp
80 918 200.11 Kbp 19 0.80 Mbp
90 0 0
100 0 0
0.840x 2241 2.18 Gbp 1265 2.20 Gbp
NG based on genome size 2.59 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 9 April 2023
aLepFus1.MT.20230409.fasta.gz (5.6 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/aLepFus1_hap1.yml (view)
species: Leptodactylus fuscus
specimen: aLepFus1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Leptodactylus_fuscus/aLepFus1/assembly_vgp_HiC_2.0/aLepFus1.HiC.hap1.20230421.fasta.gz
hap2: s3://genomeark/species/Leptodactylus_fuscus/aLepFus1/assembly_vgp_HiC_2.0/aLepFus1.HiC.hap2.20230421.fasta.gz
pretext_hap1: s3://genomeark/species/Leptodactylus_fuscus/aLepFus1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/aLepFus1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Leptodactylus_fuscus/aLepFus1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/aLepFus1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Leptodactylus_fuscus/aLepFus1/assembly_vgp_HiC_2.0/evaluation/merqury/aLepFus1_png/
pacbio_read_dir: s3://genomeark/species/Leptodactylus_fuscus/aLepFus1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Leptodactylus_fuscus/aLepFus1/genomic_data/arima/
bionano_cmap_dir: s3://genomeark/species/Leptodactylus_fuscus/aLepFus1/genomic_data/bionano/
mito: s3://genomeark/species/Leptodactylus_fuscus/aLepFus1/assembly_MT_rockefeller/aLepFus1.MT.20230409.fasta.gz
pipeline:
  - hifiasm (0.18.8+galaxy1)
  - solve (3.7)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of aLepFus1, resulting in two complete haplotypes. This individual had bionano data. HiC scaffolding was performed with yahs. K-mer spectra indicates a homogametic specimen. The HiC prep was Arima kit 2. I am submitting both hap1 & hap2 for dual curation. This is the curation ticket for hap1. 
assembly_vgp_HiC_2.0/aLepFus1_hap2.yml (view)
species: Leptodactylus fuscus
specimen: aLepFus1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Leptodactylus_fuscus/aLepFus1/assembly_vgp_HiC_2.0/aLepFus1.HiC.hap1.20230421.fasta.gz
hap2: s3://genomeark/species/Leptodactylus_fuscus/aLepFus1/assembly_vgp_HiC_2.0/aLepFus1.HiC.hap2.20230421.fasta.gz
pretext_hap1: s3://genomeark/species/Leptodactylus_fuscus/aLepFus1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/aLepFus1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Leptodactylus_fuscus/aLepFus1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/aLepFus1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Leptodactylus_fuscus/aLepFus1/assembly_vgp_HiC_2.0/evaluation/merqury/aLepFus1_png/
pacbio_read_dir: s3://genomeark/species/Leptodactylus_fuscus/aLepFus1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Leptodactylus_fuscus/aLepFus1/genomic_data/arima/
bionano_cmap_dir: s3://genomeark/species/Leptodactylus_fuscus/aLepFus1/genomic_data/bionano/
mito: s3://genomeark/species/Leptodactylus_fuscus/aLepFus1/assembly_MT_rockefeller/aLepFus1.MT.20230409.fasta.gz
pipeline:
  - hifiasm (0.18.8+galaxy1)
  - solve (3.7)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of aLepFus1, resulting in two complete haplotypes. This individual had bionano data. HiC scaffolding was performed with yahs. K-mer spectra indicates a homogametic specimen. The HiC prep was Arima kit 2. 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.