Scaphiopus couchii

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


No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) aScaCou1 35.27 Gbp N/A 26.1 GiB
Arima aScaCou1 62.17 Gbp N/A 32.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 September 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aScaCou1 PacBio HiFi (.fq) 35.27 Gbp N/A 26.1 GiB
Arima 62.17 Gbp N/A 32.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 September 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 13 August 2024
aScaCou1.HiC.hap1.20240813.fasta.gz (281.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 42.00 Mbp 1 152.48 Mbp
20 6 22.69 Mbp 2 117.40 Mbp
30 12 13.32 Mbp 3 115.83 Mbp
40 21 10.46 Mbp 4 112.92 Mbp
50 31 8.58 Mbp 5 100.90 Mbp
60 45 5.77 Mbp 6 89.99 Mbp
70 69 2.99 Mbp 7 49.06 Mbp
80 118 1.44 Mbp 10 32.57 Mbp
90 244 439.77 Kbp 13 20.77 Mbp
100 1168 17.97 Kbp 631 17.97 Kbp
1.000x 1168 1.02 Gbp 631 1.03 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 13 August 2024
aScaCou1.HiC.hap2.20240813.fasta.gz (284.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 21.30 Mbp 1 112.94 Mbp
20 11 15.75 Mbp 2 111.73 Mbp
30 18 13.34 Mbp 3 111.39 Mbp
40 28 10.50 Mbp 4 99.90 Mbp
50 39 7.21 Mbp 5 98.62 Mbp
60 57 4.77 Mbp 7 69.88 Mbp
70 90 2.37 Mbp 9 45.41 Mbp
80 160 1.10 Mbp 12 29.09 Mbp
90 317 403.03 Kbp 21 2.09 Mbp
100 1096 21.30 Kbp 528 21.56 Kbp
1.000x 1096 1.06 Gbp 528 1.06 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 19 February 2024
aScaCou1.MT.20240219.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/aScaCou1.yml (view)
species: Scaphiopus couchii
specimen: aScaCou1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Scaphiopus_couchii/aScaCou1/assembly_vgp_trio_2.0/aScaCou1.HiC.hap1.20240813.fasta.gz
hap2: s3://genomeark/species/Scaphiopus_couchii/aScaCou1/assembly_vgp_trio_2.0/aScaCou1.HiC.hap2.20240813.fasta.gz
kmer_spectra_img: s3://genomeark/species/Scaphiopus_couchii/aScaCou1/assembly_vgp_trio_2.0/evaluation/merqury/aScaCou1_png/
pacbio_read_dir: s3://genomeark/species/Scaphiopus_couchii/aScaCou1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Scaphiopus_couchii/aScaCou1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.9+galaxy0)
  - solve (3.7.0+galaxy3)
  - yahs (1.2a.2+galaxy1)
notes: This was a HiC-phased assembly of aScaCou1, resulting in two phased haplotypes. The assemblies underwent Bionano & HiC (Arima) scaffolding. The HiC library prep kit was Arima, so 5bp need to be trimmed before use.
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.