Strix aluco

Tawny owl

Included in the VGP.

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


metadata.yaml (view) (edit on github)
species:
  short_name: bStrAlu
  name: Strix aluco
  taxon_id: 111821
  common_name: Tawny owl
  order:
    name: Strigiformes
  family:
    name: Strigidae
  individuals:
    - short_name: bStrAlu2
      biosample_id: SAMEA114594455
      sex:
  genome_size: 1555020000
  genome_size_method: GoaT
  project: [ vgp ]
No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bStrAlu1 60.81 Gbp 39.11x 41.5 GiB
PacBio HiFi (.bam) bStrAlu2 80.80 Gbp 51.96x 28.0 GiB
Arima bStrAlu1 96.51 Gbp 62.06x 49.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.56 Gbp.
Last upload on 15 March 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bStrAlu1 PacBio HiFi (.fq) 60.81 Gbp 39.11x 41.5 GiB
Arima 96.51 Gbp 62.06x 49.0 GiB
bStrAlu2 PacBio HiFi (.bam) 80.80 Gbp 51.96x 28.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.56 Gbp.
Last upload on 15 March 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 22 July 2023
bStrAlu1.hap1.cur.20230722.fasta.gz (379.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 32.99 Mbp 1 173.08 Mbp
20 9 25.64 Mbp 2 138.11 Mbp
30 15 20.54 Mbp 3 133.21 Mbp
40 23 16.58 Mbp 4 132.25 Mbp
50 32 12.12 Mbp 6 89.39 Mbp
60 46 9.67 Mbp 8 45.34 Mbp
70 63 6.18 Mbp 12 29.28 Mbp
80 92 3.78 Mbp 18 22.21 Mbp
90 142 2.09 Mbp 26 10.63 Mbp
100 480 3.10 Kbp 200 20.89 Kbp
1.000x 480 1.41 Gbp 200 1.41 Gbp
NG based on genome size 1.56 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 22 July 2023
bStrAlu1.hap2.cur.20230722.fasta.gz (336.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 36.35 Mbp 1 173.56 Mbp
20 6 27.04 Mbp 2 137.13 Mbp
30 11 21.91 Mbp 3 132.98 Mbp
40 18 17.92 Mbp 4 132.66 Mbp
50 25 13.78 Mbp 5 89.68 Mbp
60 34 12.40 Mbp 7 42.50 Mbp
70 47 8.06 Mbp 10 26.39 Mbp
80 66 4.84 Mbp 15 21.93 Mbp
90 102 2.33 Mbp 23 10.85 Mbp
100 387 14.22 Kbp 182 14.22 Kbp
1.000x 387 1.21 Gbp 182 1.22 Gbp
NG based on genome size 1.56 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 13 February 2023
bStrAlu1.MT.20230213.fasta.gz (5.8 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bStrAlu1_hap1.yml (view)
species: Strix aluco
specimen: bStrAlu1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Strix_aluco/bStrAlu1/assembly_vgp_HiC_2.0/bStrAlu1.HiC.hap1.20230506.fasta.gz
hap2: s3://genomeark/species/Strix_aluco/bStrAlu1/assembly_vgp_HiC_2.0/bStrAlu1.HiC.hap2.20230506.fasta.gz
pretext_hap1: s3://genomeark/species/Strix_aluco/bStrAlu1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bStrAlu1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Strix_aluco/bStrAlu1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bStrAlu1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Strix_aluco/bStrAlu1/assembly_vgp_HiC_2.0/evaluation/merqury_postpurge/bStrAlu1_png/
mito: s3://genomeark/species/Strix_aluco/bStrAlu1/assembly_MT_rockefeller/bStrAlu1.MT.20230213.fasta.gz
mito_gb: s3://genomeark/species/Strix_aluco/bStrAlu1/assembly_MT_rockefeller/bStrAlu1.MT.20230213.gb
pacbio_read_dir: s3://genomeark/species/Strix_aluco/bStrAlu1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Strix_aluco/bStrAlu1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Strix_aluco/bStrAlu1/genomic_data/arima/
pipeline:
  - hifiasm (0.18.5+galaxy1)
  - purge_dups (1.2.6+galaxy0)
  - solve (3.7)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of bStrAlu1, resulting in two complete haplotypes. This individual did have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. I am submitting both hap1 & hap2 for dual curation. This is the curation ticket for hap1. 
assembly_vgp_HiC_2.0/bStrAlu1_hap2.yml (view)
species: Strix aluco
specimen: bStrAlu1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Strix_aluco/bStrAlu1/assembly_vgp_HiC_2.0/bStrAlu1.HiC.hap1.20230506.fasta.gz
hap2: s3://genomeark/species/Strix_aluco/bStrAlu1/assembly_vgp_HiC_2.0/bStrAlu1.HiC.hap2.20230506.fasta.gz
pretext_hap1: s3://genomeark/species/Strix_aluco/bStrAlu1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bStrAlu1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Strix_aluco/bStrAlu1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bStrAlu1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Strix_aluco/bStrAlu1/assembly_vgp_HiC_2.0/evaluation/merqury_postpurge/bStrAlu1_png/
mito: s3://genomeark/species/Strix_aluco/bStrAlu1/assembly_MT_rockefeller/bStrAlu1.MT.20230213.fasta.gz
mito_gb: s3://genomeark/species/Strix_aluco/bStrAlu1/assembly_MT_rockefeller/bStrAlu1.MT.20230213.gb
pacbio_read_dir: s3://genomeark/species/Strix_aluco/bStrAlu1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Strix_aluco/bStrAlu1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Strix_aluco/bStrAlu1/genomic_data/arima/
pipeline:
  - hifiasm (0.18.5+galaxy1)
  - purge_dups (1.2.6+galaxy0)
  - solve (3.7)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of bStrAlu1, resulting in two complete haplotypes. This individual did have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. I am submitting both hap1 & hap2 for dual curation. This is the curation 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.