Anolis sagrei

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Resource Maternal Assembly Paternal Assembly
GenBank rAnoSag1: GCA_037176765.1 rAnoSag1: GCA_037176775.1
ENA rAnoSag1: GCA_037176765.1 rAnoSag1: GCA_037176775.1
UCSC Genome Browser rAnoSag1: GCA_037176765.1 rAnoSag1: GCA_037176775.1

CC BY 2.0 gailhampshire (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) rAnoSag1 1313.76 Gbp N/A 2.2 TiB
PacBio HiFi (.fq) rAnoSag1 68.08 Gbp N/A 53.2 GiB
PacBio HiFi (.bam) rAnoSag1 206.76 Gbp N/A 719.0 GiB
Arima rAnoSag1 86.16 Gbp N/A 42.6 GiB
Illumina rAnoSag2 117.81 Gbp N/A 54.8 GiB
rAnoSag3 123.45 Gbp N/A 57.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 6 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rAnoSag1 PacBio HiFi (subreads) 1313.76 Gbp N/A 2.2 TiB
PacBio HiFi (.fq) 68.08 Gbp N/A 53.2 GiB
PacBio HiFi (.bam) 206.76 Gbp N/A 719.0 GiB
Arima 86.16 Gbp N/A 42.6 GiB
rAnoSag2 Illumina 117.81 Gbp N/A 54.8 GiB
rAnoSag3 Illumina 123.45 Gbp N/A 57.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 6 June 2024.
Assemblies

No assemblies.

Assembly Metadata
assembly_vgp_trio_2.0/rAnoSag1_mat.yml (view)
species: Anolis sagrei
specimen: rAnoSag1
projects: 
  - vgp
data_location: S3
release_to: S3
maternal: s3://genomeark/species/Anolis_sagrei/rAnoSag1/assembly_vgp_trio_2.0/rAnoSag1.trio.mat.20231222.fasta.gz
pretext: s3://genomeark/species/Anolis_sagrei/rAnoSag1/assembly_vgp_trio_2.0/evaluation/hap2/pretext/rAnoSag1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Anolis_sagrei/rAnoSag1/assembly_vgp_trio_2.0/evaluation/merqury/rAnoSag1_png/
pacbio_read_dir: s3://genomeark/species/Anolis_sagrei/rAnoSag1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Anolis_sagrei/rAnoSag1/genomic_data/arima/
pipeline:
  - hifiasm (0.19.7+galaxy1), with trio-dual parameter on
  - purge_dups (2.2)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a trio assembly of rAnoSag1 (internal ID: VGL-rAnoSag4) using parental illumina data and hifiasm in trio mode with the "trio-dual" parameter on. 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. In the intermediate files, hap1 is the paternal haplotype and hap2 is the maternal haplotype. Both haplotypes individually went through a round of purge_dups. We are submitting both haplotypes for trio curation, and this is the ticket for the maternal haplotype (hap2).
assembly_vgp_trio_2.0/rAnoSag1_pat.yml (view)
species: Anolis sagrei
specimen: rAnoSag1
projects: 
  - vgp
data_location: S3
release_to: S3
paternal: s3://genomeark/species/Anolis_sagrei/rAnoSag1/assembly_vgp_trio_2.0/rAnoSag1.trio.pat.20231222.fasta.gz
pretext: s3://genomeark/species/Anolis_sagrei/rAnoSag1/assembly_vgp_trio_2.0/evaluation/hap2/pretext/rAnoSag1_hap1__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Anolis_sagrei/rAnoSag1/assembly_vgp_trio_2.0/evaluation/merqury/rAnoSag1_png/
pacbio_read_dir: s3://genomeark/species/Anolis_sagrei/rAnoSag1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Anolis_sagrei/rAnoSag1/genomic_data/arima/
pipeline:
  - hifiasm (0.19.7+galaxy1), with trio-dual parameter on
  - purge_dups (2.2)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a trio assembly of rAnoSag1 (internal ID: VGL-rAnoSag4) using parental illumina data and hifiasm in trio mode with the "trio-dual" parameter on. 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. In the intermediate files, hap1 is the paternal haplotype and hap2 is the maternal haplotype. Both haplotypes individually went through a round of purge_dups. We are submitting both haplotypes for trio curation, and this is the ticket for the paternal haplotype (hap1).
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.