Scaphiopus couchii

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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_curated from 17 November 2025
aScaCou1.hap1.cur.20251117.fasta.gz (280.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 25.95 Mbp 1 144.22 Mbp
20 7 22.69 Mbp 2 118.37 Mbp
30 14 13.30 Mbp 3 118.11 Mbp
40 22 10.46 Mbp 4 113.88 Mbp
50 33 8.56 Mbp 5 101.87 Mbp
60 47 5.77 Mbp 6 96.50 Mbp
70 71 2.99 Mbp 7 51.25 Mbp
80 121 1.44 Mbp 9 44.61 Mbp
90 247 426.62 Kbp 12 28.89 Mbp
100 1182 2.96 Kbp 577 17.97 Kbp
1.000x 1182 1.01 Gbp 577 1.03 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 17 November 2025
aScaCou1.hap2.cur.20251117.fasta.gz (258.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 21.30 Mbp 1 138.71 Mbp
20 11 15.75 Mbp 2 119.35 Mbp
30 18 13.34 Mbp 3 114.05 Mbp
40 28 10.43 Mbp 4 112.99 Mbp
50 40 7.04 Mbp 5 101.22 Mbp
60 59 4.26 Mbp 6 96.97 Mbp
70 93 2.30 Mbp 8 49.96 Mbp
80 163 1.10 Mbp 10 35.52 Mbp
90 322 398.59 Kbp 14 16.98 Mbp
100 1114 651 bp 494 22.16 Kbp
1.000x 1114 1.06 Gbp 494 1.07 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.