Eleutherodactylus coqui

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) aEleCoq1 119.52 Gbp N/A 91.9 GiB
Arima aEleCoq1 586.19 Gbp N/A 279.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 15 August 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aEleCoq1 PacBio HiFi (.fq) 119.52 Gbp N/A 91.9 GiB
Arima 586.19 Gbp N/A 279.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 15 August 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 7 October 2023
aEleCoq1.hap1.cur.20231007.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 8 30.80 Mbp 1 0.54 Gbp
20 21 21.05 Mbp 2 346.26 Mbp
30 38 18.10 Mbp 3 319.81 Mbp
40 60 13.62 Mbp 4 304.12 Mbp
50 89 10.39 Mbp 5 277.44 Mbp
60 126 8.00 Mbp 6 246.83 Mbp
70 179 5.26 Mbp 8 210.11 Mbp
80 257 3.46 Mbp 10 143.70 Mbp
90 394 1.72 Mbp 12 132.95 Mbp
100 1615 10.59 Kbp 956 10.59 Kbp
1.000x 1615 3.37 Gbp 956 3.37 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 7 October 2023
aEleCoq1.hap2.cur.20231007.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 39.08 Mbp 1 0.53 Gbp
20 17 25.65 Mbp 2 334.35 Mbp
30 32 18.98 Mbp 3 315.19 Mbp
40 54 12.96 Mbp 4 308.51 Mbp
50 84 10.01 Mbp 5 286.58 Mbp
60 122 7.74 Mbp 6 249.86 Mbp
70 176 5.01 Mbp 8 212.34 Mbp
80 260 3.34 Mbp 10 150.57 Mbp
90 400 1.68 Mbp 12 133.18 Mbp
100 1512 9.38 Kbp 827 9.38 Kbp
1.000x 1512 3.36 Gbp 827 3.36 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 15 August 2023
aEleCoq1.MT.20230815.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/aEleCoq1_hap1.yml (view)
species: Eleutherodactylus coqui
specimen: aEleCoq1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Eleutherodactylus_coqui/aEleCoq1/assembly_vgp_HiC_2.0/aEleCoq1.HiC.hap1.20230815.fasta.gz
hap2: s3://genomeark/species/Eleutherodactylus_coqui/aEleCoq1/assembly_vgp_HiC_2.0/aEleCoq1.HiC.hap2.20230815.fasta.gz
pretext_hap1: s3://genomeark/species/Eleutherodactylus_coqui/aEleCoq1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/aEleCoq1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Eleutherodactylus_coqui/aEleCoq1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/aEleCoq1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Eleutherodactylus_coqui/aEleCoq1/assembly_vgp_HiC_2.0/evaluation/merqury/aEleCoq1_png/
mito: s3://genomeark/species/Eleutherodactylus_coqui/aEleCoq1/assembly_MT_rockefeller/aEleCoq1.MT.20230815.fasta.gz
pacbio_read_dir: s3://genomeark/species/Eleutherodactylus_coqui/aEleCoq1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Eleutherodactylus_coqui/aEleCoq1/genomic_data/arima/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of aEleCoq1 (VGL ID is aEleCoq3), resulting in two complete haplotypes. The provider listed the sample as male, and the kmer spectra seem to support a homogametic specimen. This individual did not bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. This is a phase 1 species. We are submitting both haplotypes for dual curation, and this is the ticket for hap1. 
assembly_vgp_HiC_2.0/aEleCoq1_hap2.yml (view)
species: Eleutherodactylus coqui
specimen: aEleCoq1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Eleutherodactylus_coqui/aEleCoq1/assembly_vgp_HiC_2.0/aEleCoq1.HiC.hap1.20230815.fasta.gz
hap2: s3://genomeark/species/Eleutherodactylus_coqui/aEleCoq1/assembly_vgp_HiC_2.0/aEleCoq1.HiC.hap2.20230815.fasta.gz
pretext_hap1: s3://genomeark/species/Eleutherodactylus_coqui/aEleCoq1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/aEleCoq1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Eleutherodactylus_coqui/aEleCoq1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/aEleCoq1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Eleutherodactylus_coqui/aEleCoq1/assembly_vgp_HiC_2.0/evaluation/merqury/aEleCoq1_png/
mito: s3://genomeark/species/Eleutherodactylus_coqui/aEleCoq1/assembly_MT_rockefeller/aEleCoq1.MT.20230815.fasta.gz
pacbio_read_dir: s3://genomeark/species/Eleutherodactylus_coqui/aEleCoq1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Eleutherodactylus_coqui/aEleCoq1/genomic_data/arima/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of aEleCoq1 (VGL ID is aEleCoq3), resulting in two complete haplotypes. The provider listed the sample as male, and the kmer spectra seem to support a homogametic specimen. This individual did not bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. This is a phase 1 species. We are submitting both haplotypes for dual curation, and this is the 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.