Liasis olivaceus

olive python

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  name: Liasis olivaceus
  individuals:
  - short_name: rLiaOli1
  short_name: rLiaOli
  taxon_id: 283338
  common_name: olive python
  genome_size: 1675000000
  genome_size_method: GoAT
  order:
    name: Squamata
  family:
    name: Pythonidae
  project: [ vgp ]
CC BY-SA 4.0 Wallacegromit1 (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) rLiaOli1 225.90 Gbp 134.86x 554.5 GiB
rLiaOli2 450.02 Gbp 268.67x 783.2 GiB
PacBio HiFi (.fq) rLiaOli1 56.08 Gbp 33.48x 44.7 GiB
rLiaOli2 83.38 Gbp 49.78x 46.2 GiB
PacBio HiFi (.bam) rLiaOli1 55.82 Gbp 33.32x 194.1 GiB
rLiaOli2 449.04 Gbp 268.08x 230.9 GiB
Oxford Nanopore Simplex rLiaOli1 40.22 Gbp 24.01x 33.3 GiB
Bionano rLiaOli1 N/A 685.08x 2.1 GiB
Arima rLiaOli1 170.49 Gbp 101.78x 82.8 GiB
rLiaOli2 302.74 Gbp 180.74x 139.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.68 Gbp.
Last upload on 4 September 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rLiaOli1 PacBio HiFi (subreads) 225.90 Gbp 134.86x 554.5 GiB
PacBio HiFi (.fq) 56.08 Gbp 33.48x 44.7 GiB
PacBio HiFi (.bam) 55.82 Gbp 33.32x 194.1 GiB
Oxford Nanopore Simplex 40.22 Gbp 24.01x 33.3 GiB
Bionano N/A 685.08x 2.1 GiB
Arima 170.49 Gbp 101.78x 82.8 GiB
rLiaOli2 PacBio HiFi (subreads) 450.02 Gbp 268.67x 783.2 GiB
PacBio HiFi (.fq) 83.38 Gbp 49.78x 46.2 GiB
PacBio HiFi (.bam) 449.04 Gbp 268.08x 230.9 GiB
Arima 302.74 Gbp 180.74x 139.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.68 Gbp.
Last upload on 4 September 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 14 December 2022
rLiaOli1.hap1.cur.20221214.fasta.gz (428.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 203.66 Mbp 1 332.08 Mbp
20 3 104.46 Mbp 2 264.61 Mbp
30 4 98.00 Mbp 2 264.61 Mbp
40 7 72.83 Mbp 3 203.66 Mbp
50 9 62.16 Mbp 4 116.16 Mbp
60 13 32.12 Mbp 5 113.56 Mbp
70 19 23.73 Mbp 7 82.07 Mbp
80 30 11.54 Mbp 10 26.30 Mbp
90 0 0
100 0 0
0.887x 116 1.49 Gbp 43 1.49 Gbp
NG based on genome size 1.68 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 14 December 2022
rLiaOli1.hap2.cur.20221214.fasta.gz (425.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 203.54 Mbp 1 332.68 Mbp
20 3 104.43 Mbp 2 259.48 Mbp
30 4 96.37 Mbp 2 259.48 Mbp
40 6 74.90 Mbp 3 203.54 Mbp
50 9 56.84 Mbp 4 116.90 Mbp
60 13 32.11 Mbp 5 113.50 Mbp
70 22 12.89 Mbp 7 81.91 Mbp
80 41 6.18 Mbp 11 25.60 Mbp
90 0 0
100 0 0
0.880x 158 1.47 Gbp 65 1.48 Gbp
NG based on genome size 1.68 Gbp.
Individual 2 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 23 January 2024
rLiaOli2.HiC.hap1.20240123.fasta.gz (428.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 203.78 Mbp 1 332.01 Mbp
20 2 165.90 Mbp 2 261.06 Mbp
30 3 155.55 Mbp 2 261.06 Mbp
40 5 98.25 Mbp 3 203.78 Mbp
50 7 87.14 Mbp 4 118.95 Mbp
60 9 74.73 Mbp 5 116.06 Mbp
70 11 58.95 Mbp 7 97.68 Mbp
80 18 15.48 Mbp 9 77.04 Mbp
90 0 0
100 0 0
0.887x 82 1.49 Gbp 52 1.49 Gbp
NG based on genome size 1.68 Gbp.
Individual 2 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 23 January 2024
rLiaOli2.HiC.hap2.20240123.fasta.gz (426.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 155.37 Mbp 1 330.43 Mbp
20 3 134.64 Mbp 2 259.70 Mbp
30 4 109.92 Mbp 2 259.70 Mbp
40 6 79.94 Mbp 3 203.11 Mbp
50 8 53.34 Mbp 4 140.49 Mbp
60 12 36.69 Mbp 5 115.94 Mbp
70 17 28.58 Mbp 7 96.72 Mbp
80 26 12.68 Mbp 8 82.02 Mbp
90 0 0
100 0 0
0.882x 97 1.48 Gbp 55 1.48 Gbp
NG based on genome size 1.68 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/rLiaOli1.yml (view)
species: Liasis olivaceus
specimen: rLiaOli1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Liasis_olivaceus/rLiaOli1/assembly_vgp_HiC_2.0/rLiaOli1.HiC.hap1.20221214.fasta.gz
hap2: s3://genomeark/species/Liasis_olivaceus/rLiaOli1/assembly_vgp_HiC_2.0/rLiaOli1.HiC.hap2.20221214.fasta.gz
pretext_hap1: s3://genomeark/species/Liasis_olivaceus/rLiaOli1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/rLiaOli1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Liasis_olivaceus/rLiaOli1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rLiaOli1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Liasis_olivaceus/rLiaOli1/assembly_vgp_HiC_2.0/evaluation/merqury/rLiaOli1_png/
pacbio_read_dir: s3://genomeark/species/Liasis_olivaceus/rLiaOli1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Liasis_olivaceus/rLiaOli1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Liasis_olivaceus/rLiaOli1/genomic_data/arima/
pipeline: 
  - hifiasm (0.16.1+galaxy4)
  - solve (3.7)
  - yahs (1.2a.2+galaxy0)
notes: This was a Hifiasm-HiC assembly of rLiaOli1, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Swift-IDT. 
assembly_vgp_HiC_2.0/rLiaOli2.yml (view)
species: Liasis olivaceus
specimen: rLiaOli2
projects: 
  - vgp
data_location: S3
release_to: S3
hap1: s3://genomeark/species/Liasis_olivaceus/rLiaOli2/assembly_vgp_HiC_2.0/rLiaOli2.HiC.hap1.20240123.fasta.gz
hap2: s3://genomeark/species/Liasis_olivaceus/rLiaOli2/assembly_vgp_HiC_2.0/rLiaOli2.HiC.hap2.20240123.fasta.gz
pretext_hap1: s3://genomeark/species/Liasis_olivaceus/rLiaOli2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/rLiaOli2_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Liasis_olivaceus/rLiaOli2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rLiaOli2_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Liasis_olivaceus/rLiaOli2/assembly_vgp_HiC_2.0/evaluation/merqury/rLiaOli2_png/
pacbio_read_dir: s3://genomeark/species/Liasis_olivaceus/rLiaOli2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Liasis_olivaceus/rLiaOli2/genomic_data/arima/
bionano_cmap_dir: s3://genomeark/species/Liasis_olivaceus/rLiaOli2/genomic_data/bionano/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of rLiaOli2, resulting in two complete haplotypes. This individual did have bionano data, but it was not used during assembly because the HiC scaffolding was sufficient. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2, and the library prep kit was the Arima kit, requiring 5 bp trimmed off both forward and reverse reads before usage with the Arima mapping pipeline. MitoHiFi failed to find a mito for this individual's data.  
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.