Tiliqua scincoides

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) rTilSci1 1010.65 Gbp N/A 1.7 TiB
PacBio HiFi (.fq) rTilSci1 51.45 Gbp N/A 41.2 GiB
PacBio HiFi (.bam) rTilSci1 158.87 Gbp N/A 551.1 GiB
Arima rTilSci1 121.48 Gbp N/A 58.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 13 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rTilSci1 PacBio HiFi (subreads) 1010.65 Gbp N/A 1.7 TiB
PacBio HiFi (.fq) 51.45 Gbp N/A 41.2 GiB
PacBio HiFi (.bam) 158.87 Gbp N/A 551.1 GiB
Arima 121.48 Gbp N/A 58.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 13 June 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 8 August 2023
rTilSci1.hap1.cur.20230808.fasta.gz (493.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 112.10 Mbp 1 314.85 Mbp
20 3 97.34 Mbp 2 282.99 Mbp
30 5 57.77 Mbp 2 282.99 Mbp
40 9 49.85 Mbp 3 237.25 Mbp
50 12 38.98 Mbp 4 220.63 Mbp
60 19 23.24 Mbp 4 220.63 Mbp
70 27 15.83 Mbp 5 147.12 Mbp
80 45 6.72 Mbp 7 80.78 Mbp
90 90 2.27 Mbp 10 41.40 Mbp
100 1113 1.67 Kbp 827 14.02 Kbp
1.000x 1113 1.69 Gbp 827 1.69 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 8 August 2023
rTilSci1.hap2.cur.20230808.fasta.gz (473.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 96.78 Mbp 1 314.32 Mbp
20 4 81.08 Mbp 2 272.45 Mbp
30 6 57.70 Mbp 2 272.45 Mbp
40 9 46.53 Mbp 3 242.16 Mbp
50 14 33.11 Mbp 3 242.16 Mbp
60 19 26.12 Mbp 4 224.94 Mbp
70 27 15.53 Mbp 5 144.32 Mbp
80 46 5.52 Mbp 7 80.22 Mbp
90 97 1.91 Mbp 9 48.70 Mbp
100 722 14.02 Kbp 350 14.02 Kbp
1.000x 722 1.62 Gbp 350 1.62 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/rTilSci1_hap1.yml (view)
species: Tiliqua scincoides
specimen: rTilSci1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Tiliqua_scincoides/rTilSci1/assembly_vgp_HiC_2.0/rTilSci1.HiC.hap1.20230411.fasta.gz
hap2: s3://genomeark/species/Tiliqua_scincoides/rTilSci1/assembly_vgp_HiC_2.0/rTilSci1.HiC.hap2.20230411.fasta.gz
pretext_hap1: s3://genomeark/species/Tiliqua_scincoides/rTilSci1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/rTilSci1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Tiliqua_scincoides/rTilSci1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rTilSci1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Tiliqua_scincoides/rTilSci1/assembly_vgp_HiC_2.0/evaluation/merqury/rTilSci1_png/
pacbio_read_dir: s3://genomeark/species/Tiliqua_scincoides/rTilSci1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Tiliqua_scincoides/rTilSci1/genomic_data/arima/
pipeline:
  - hifiasm (0.18.5+galaxy1)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of rTilSci1, resulting in two complete haplotypes. This individual did not 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. Please note that both haplotypes show some false joins after yahs scaffolding. I tried to re-run yahs with different resolutions, but could not obtain a satisfactory result.
assembly_vgp_HiC_2.0/rTilSci1_hap2.yml (view)
species: Tiliqua scincoides
specimen: rTilSci1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Tiliqua_scincoides/rTilSci1/assembly_vgp_HiC_2.0/rTilSci1.HiC.hap1.20230411.fasta.gz
hap2: s3://genomeark/species/Tiliqua_scincoides/rTilSci1/assembly_vgp_HiC_2.0/rTilSci1.HiC.hap2.20230411.fasta.gz
pretext_hap1: s3://genomeark/species/Tiliqua_scincoides/rTilSci1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/rTilSci1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Tiliqua_scincoides/rTilSci1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rTilSci1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Tiliqua_scincoides/rTilSci1/assembly_vgp_HiC_2.0/evaluation/merqury/rTilSci1_png/
pacbio_read_dir: s3://genomeark/species/Tiliqua_scincoides/rTilSci1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Tiliqua_scincoides/rTilSci1/genomic_data/arima/
pipeline:
  - hifiasm (0.18.5+galaxy1)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of rTilSci1, resulting in two complete haplotypes. This individual did not 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. Please note that both haplotypes show some false joins after yahs scaffolding. I tried to re-run yahs with different resolutions, but could not obtain a satisfactory result.
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.