Engystomops pustulosus

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Resource Maternal Assembly Paternal Assembly
GenBank aEngPut4: GCA_040894005.1 aEngPut4: GCA_040894015.1
ENA aEngPut4: GCA_040894005.1 aEngPut4: GCA_040894015.1
UCSC Genome Browser aEngPut4: GCA_040894005.1 aEngPut4: GCA_040894015.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) aEngPut4 84.30 Gbp N/A 41.2 GiB
PacBio HiFi (.bam) aEngPut4 85.64 Gbp N/A 344.1 GiB
Arima aEngPut1 183.31 Gbp N/A 96.3 GiB
Illumina aEngPut2 81.38 Gbp N/A 39.9 GiB
aEngPut3 59.21 Gbp N/A 28.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 15 April 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aEngPut1 Arima 183.31 Gbp N/A 96.3 GiB
aEngPut2 Illumina 81.38 Gbp N/A 39.9 GiB
aEngPut3 Illumina 59.21 Gbp N/A 28.7 GiB
aEngPut4 PacBio HiFi (.fq) 84.30 Gbp N/A 41.2 GiB
PacBio HiFi (.bam) 85.64 Gbp N/A 344.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 15 April 2024.
Assemblies

No assemblies.

Assembly Metadata
assembly_vgp_trio_2.0/aEngPut4.yml (view)
species: Engystomops pustulosus
specimen: aEngPut4
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
maternal: s3://genomeark/species/Engystomops_pustulosus/aEngPut4/assembly_vgp_HiC_2.0/aEngPut4.trio.pat.20240502.fasta.gz
paternal: s3://genomeark/species/Engystomops_pustulosus/aEngPut4/assembly_vgp_HiC_2.0/aEngPut4.trio.mat.20240502.fasta.gz
mat_pretext: s3://genomeark/species/Engystomops_pustulosus/aEngPut4/assembly_vgp_trio_2.0/evaluation/pat/pretext/aEngPut4_hap1__s2_heatmap.pretext
pat_pretext: s3://genomeark/species/Engystomops_pustulosus/aEngPut4/assembly_vgp_trio_2.0/evaluation/mat/pretext/aEngPut4_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Engystomops_pustulosus/aEngPut4/assembly_vgp_trio_2.0/evaluation/merqury_trio_s2/aEngPut4_png/
pacbio_read_dir: s3://genomeark/species/Engystomops_pustulosus/aEngPut4/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Engystomops_pustulosus/aEngPut1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - purge_dups (1.2.6+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm trio (--trio-dual parameter on) assembly of aEngPut4, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS using HiC data from a sibling, aEngPut1. The HiC prep kit used was Arima library prep. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. Both haplotypes underwent purging to remove some false duplicates. Merqury plots suggest some diploid-coverage regions that did not segregate equally into both haplotypes, having been placed only in the maternal assembly. This is a VGP Phase 1 species we are submitting for dual curation.
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.