Ascaphus truei

tailed frog

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  name: Ascaphus truei
  individuals:
  - short_name: aAscTru4
  short_name: aAscTru
  taxon_id: 8439
  common_name: tailed frog
  genome_size: 4042000000
  genome_size_method: GoAT
  order:
    name: Anura
  family:
    name: Ascaphidae
  project: [ vgp ]
CC BY-NC 2.0 Ken-ichi Ueda (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) aAscTru1 580.51 Gbp 143.62x 1.3 TiB
PacBio HiFi (.fq) aAscTru1 118.91 Gbp 29.42x 89.0 GiB
PacBio HiFi (.bam) aAscTru1 100.40 Gbp 24.84x 342.9 GiB
Arima aAscTru1 345.81 Gbp 85.55x 167.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size 4.04 Gbp.
Last upload on 29 August 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aAscTru1 PacBio HiFi (subreads) 580.51 Gbp 143.62x 1.3 TiB
PacBio HiFi (.fq) 118.91 Gbp 29.42x 89.0 GiB
PacBio HiFi (.bam) 100.40 Gbp 24.84x 342.9 GiB
Arima 345.81 Gbp 85.55x 167.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size 4.04 Gbp.
Last upload on 29 August 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 29 April 2024
aAscTru1.hap1.cur.20240429.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 100 3.02 Mbp 1 0.56 Gbp
20 259 2.16 Mbp 2 491.29 Mbp
30 479 1.56 Mbp 3 439.62 Mbp
40 779 1.17 Mbp 4 424.00 Mbp
50 1178 0.87 Mbp 5 310.04 Mbp
60 1726 0.63 Mbp 7 117.24 Mbp
70 2513 412.32 Kbp 12 58.93 Mbp
80 3836 223.24 Kbp 21 33.18 Mbp
90 7159 57.49 Kbp 1390 81.09 Kbp
100 0 0
0.921x 9569 3.72 Gbp 3549 3.72 Gbp
NG based on genome size 4.04 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 29 April 2024
aAscTru1.hap2.cur.20240429.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 105 2.91 Mbp 1 0.53 Gbp
20 276 2.01 Mbp 2 0.51 Gbp
30 509 1.50 Mbp 3 458.98 Mbp
40 816 1.13 Mbp 4 396.16 Mbp
50 1230 0.85 Mbp 5 311.34 Mbp
60 1796 0.60 Mbp 7 118.04 Mbp
70 2635 385.09 Kbp 13 58.67 Mbp
80 4074 200.58 Kbp 21 33.73 Mbp
90 8060 38.84 Kbp 2067 46.35 Kbp
100 0 0
0.905x 8802 3.66 Gbp 2779 3.66 Gbp
NG based on genome size 4.04 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/aAscTru1_hap1.yml (view)
species: Ascaphus truei
specimen: aAscTru1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Ascaphus_truei/aAscTru1/assembly_vgp_HiC_2.0/aAscTru1.HiC.hap1.20230829.fasta.gz
hap2: s3://genomeark/species/Ascaphus_truei/aAscTru1/assembly_vgp_HiC_2.0/aAscTru1.HiC.hap2.20230829.fasta.gz
pretext_hap1: s3://genomeark/species/Ascaphus_truei/aAscTru1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/aAscTru1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Ascaphus_truei/aAscTru1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/aAscTru1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Ascaphus_truei/aAscTru1/assembly_vgp_HiC_2.0/evaluation/merqury/aAscTru1_png/
pacbio_read_dir: s3://genomeark/species/Ascaphus_truei/aAscTru1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Ascaphus_truei/aAscTru1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of aAscTru1 (VGL-aAscTru4), resulting in two complete haplotypes. HiC scaffolding was performed with YaHS. This sample did not have bionano data. 
assembly_vgp_HiC_2.0/aAscTru1_hap2.yml (view)
species: Ascaphus truei
specimen: aAscTru1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Ascaphus_truei/aAscTru1/assembly_vgp_HiC_2.0/aAscTru1.HiC.hap1.20230829.fasta.gz
hap2: s3://genomeark/species/Ascaphus_truei/aAscTru1/assembly_vgp_HiC_2.0/aAscTru1.HiC.hap2.20230829.fasta.gz
pretext_hap1: s3://genomeark/species/Ascaphus_truei/aAscTru1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/aAscTru1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Ascaphus_truei/aAscTru1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/aAscTru1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Ascaphus_truei/aAscTru1/assembly_vgp_HiC_2.0/evaluation/merqury/aAscTru1_png/
pacbio_read_dir: s3://genomeark/species/Ascaphus_truei/aAscTru1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Ascaphus_truei/aAscTru1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of aAscTru1 (VGL-aAscTru4), resulting in two complete haplotypes. HiC scaffolding was performed with YaHS. This sample did not have bionano data. 
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.