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_vgp_HiC_2.0 from 29 August 2023
aAscTru1.HiC.hap1.20230829.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 99 3.09 Mbp 1 0.50 Gbp
20 254 2.19 Mbp 2 491.63 Mbp
30 470 1.60 Mbp 3 478.05 Mbp
40 765 1.18 Mbp 4 437.14 Mbp
50 1158 0.89 Mbp 5 391.26 Mbp
60 1695 0.64 Mbp 7 116.34 Mbp
70 2463 425.20 Kbp 12 48.77 Mbp
80 3737 234.75 Kbp 62 1.81 Mbp
90 6766 68.42 Kbp 1223 103.75 Kbp
100 0 0
0.927x 9609 3.75 Gbp 3674 3.75 Gbp
NG based on genome size 4.04 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 29 August 2023
aAscTru1.HiC.hap2.20230829.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 105 2.91 Mbp 1 0.92 Gbp
20 276 2.01 Mbp 1 0.92 Gbp
30 509 1.50 Mbp 2 0.60 Gbp
40 817 1.13 Mbp 3 330.89 Mbp
50 1234 0.84 Mbp 4 184.67 Mbp
60 1810 0.58 Mbp 9 59.52 Mbp
70 2668 373.13 Kbp 17 42.34 Mbp
80 4164 190.81 Kbp 99 1.18 Mbp
90 0 0
100 0 0
0.899x 8762 3.63 Gbp 2884 3.64 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.