Xenopus petersii

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) aXenPet1 104.71 Gbp N/A 79.3 GiB
Arima aXenPet1 210.05 Gbp N/A 113.3 GiB
Illumina aXenPet2 141.64 Gbp N/A 66.1 GiB
aXenPet3 201.98 Gbp N/A 93.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 21 April 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aXenPet1 PacBio HiFi (.fq) 104.71 Gbp N/A 79.3 GiB
Arima 210.05 Gbp N/A 113.3 GiB
aXenPet2 Illumina 141.64 Gbp N/A 66.1 GiB
aXenPet3 Illumina 201.98 Gbp N/A 93.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 21 April 2023.
Assemblies
Individual 1 Maternal Assembly
Version assembly_curated from 11 March 2024
aXenPet1.mat.decon.20240311.fasta.gz (0.1 KiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 0 0
20 0 0
30 0 0
40 0 0
50 0 0
60 0 0
70 0 0
80 0 0
90 0 0
100 0 0
0.000x 0 0
NG based on genome size .
Individual 1 Paternal Assembly
Version assembly_curated from 11 March 2024
aXenPet1.pat.decon.20240311.fasta.gz (0.1 KiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 0 0
20 0 0
30 0 0
40 0 0
50 0 0
60 0 0
70 0 0
80 0 0
90 0 0
100 0 0
0.000x 0 0
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 15 August 2023
aXenPet1.MT.20230815.fasta.gz (5.7 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_trio_2.0/aXenPet1_mat.yml (view)
species: Xenopus petersii
specimen: aXenPet1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: maternal
maternal: s3://genomeark/species/Xenopus_petersii/aXenPet1/assembly_vgp_trio_2.0/aXenPet1.trio.mat.20240123.fasta.gz
pretext: s3://genomeark/species/Xenopus_petersii/aXenPet1/assembly_vgp_trio_2.0/evaluation/hap2/pretext/aXenPet1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Xenopus_petersii/aXenPet1/assembly_vgp_trio_2.0/evaluation/merqury/aXenPet1_png/
mito: s3://genomeark/species/Xenopus_petersii/aXenPet1/assembly_MT_rockefeller/aXenPet1.MT.20230815.fasta.gz
pacbio_read_dir: s3://genomeark/species/Xenopus_petersii/aXenPet1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Xenopus_petersii/aXenPet1/genomic_data/arima/
pipeline:
  - hifiasm with trio-dual (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a trio assembly (with trio-dual mode on) of aXenPet1 using parental illumina data. This individual was previously curated without trio-dual mode, but the assembly was run again with trio-dual on and looks much better. Sample metadata says a female specimen. This individual did not have 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. In the intermediate files, hap1 is the paternal haplotype and hap2 is the maternal haplotype. We are submitting both haplotypes for trio curation, and this is the ticket for the maternal haplotype.
assembly_vgp_trio_2.0/aXenPet1_pat.yml (view)
species: Xenopus petersii
specimen: aXenPet1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: paternal
paternal: s3://genomeark/species/Xenopus_petersii/aXenPet1/assembly_vgp_trio_2.0/aXenPet1.trio.pat.20240123.fasta.gz
pretext: s3://genomeark/species/Xenopus_petersii/aXenPet1/assembly_vgp_trio_2.0/evaluation/hap1/pretext/aXenPet1_hap1__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Xenopus_petersii/aXenPet1/assembly_vgp_trio_2.0/evaluation/merqury/aXenPet1_png/
mito: s3://genomeark/species/Xenopus_petersii/aXenPet1/assembly_MT_rockefeller/aXenPet1.MT.20230815.fasta.gz
pacbio_read_dir: s3://genomeark/species/Xenopus_petersii/aXenPet1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Xenopus_petersii/aXenPet1/genomic_data/arima/
pipeline:
  - hifiasm with trio-dual (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a trio assembly (with trio-dual mode on) of aXenPet1 using parental illumina data. This individual was previously curated without trio-dual mode, but the assembly was run again with trio-dual on and looks much better. Sample metadata says a female specimen. This individual did not have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The trio reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. In the intermediate files, hap1 is the paternal haplotype and hap2 is the maternal haplotype. We are submitting both haplotypes for trio curation, and this is the ticket for the paternal haplotype. 
assembly_vgp_trio_2.0_hifiasm0.16.1-r375/aXenPet1_mat.yml (view)
species: Xenopus petersii
specimen: aXenPet1
projects: 
  - vgp
data_location: S3
release_to: S3
maternal: s3://genomeark/species/Xenopus_petersii/aXenPet1/assembly_vgp_HiC_2.0/aXenPet1.trio.mat.20230815.fasta.gz
pretext: s3://genomeark/species/Xenopus_petersii/aXenPet1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/aXenPet1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Xenopus_petersii/aXenPet1/assembly_vgp_HiC_2.0/evaluation/merqury/aXenPet1_png/
mito: s3://genomeark/species/Xenopus_petersii/aXenPet1/assembly_MT_rockefeller/aXenPet1.MT.20230815.fasta.gz
pacbio_read_dir: s3://genomeark/species/Xenopus_petersii/aXenPet1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Xenopus_petersii/aXenPet1/genomic_data/arima/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - purge_dups (2.2) for paternal haplotype
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a trio assembly of aXenPet1 using parental illumina data. Sample metadata says a female specimen. This individual did not have 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. In the intermediate files, hap1 is the paternal haplotype and hap2 is the maternal haplotype. The paternal haplotype went through purge_dups due to presence of 2-copy k-mers at diploid coverage in the merqury plots. The BUSCO values were troublesome, and likely indicate presence of many paralogs. We are submitting both haplotypes for trio curation, and this is the ticket for the maternal haplotype.
assembly_vgp_trio_2.0_hifiasm0.16.1-r375/aXenPet1_pat.yml (view)
species: Xenopus petersii
specimen: aXenPet1
projects: 
  - vgp
data_location: S3
release_to: S3
paternal: s3://genomeark/species/Xenopus_petersii/aXenPet1/assembly_vgp_HiC_2.0/aXenPet1.trio.pat.20230815.fasta.gz
pretext: s3://genomeark/species/Xenopus_petersii/aXenPet1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/aXenPet1_hap1__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Xenopus_petersii/aXenPet1/assembly_vgp_HiC_2.0/evaluation/merqury/aXenPet1_png/
mito: s3://genomeark/species/Xenopus_petersii/aXenPet1/assembly_MT_rockefeller/aXenPet1.MT.20230815.fasta.gz
pacbio_read_dir: s3://genomeark/species/Xenopus_petersii/aXenPet1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Xenopus_petersii/aXenPet1/genomic_data/arima/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - purge_dups (2.2) for paternal haplotype
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a trio assembly of aXenPet1 using parental illumina data. Sample metadata says a female specimen. This individual did not have 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. In the intermediate files, hap1 is the paternal haplotype and hap2 is the maternal haplotype. The paternal haplotype went through purge_dups due to presence of 2-copy k-mers at diploid coverage in the merqury plots. The BUSCO values were troublesome, and likely indicate presence of many paralogs. We are submitting both haplotypes for trio curation, and this is the ticket for the paternal haplotype.
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.