Sternotherus odoratus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) rSteOdo2 165.31 Gbp 94.71x 105.3 GiB
PacBio HiFi (.bam) rSteOdo2 107.57 Gbp 61.63x 299.9 GiB
Arima rSteOdo2 108.24 Gbp 62.01x 55.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.75 Gbp.
Last upload on 20 August 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rSteOdo2 PacBio HiFi (.fq) 165.31 Gbp 94.71x 105.3 GiB
PacBio HiFi (.bam) 107.57 Gbp 61.63x 299.9 GiB
Arima 108.24 Gbp 62.01x 55.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.75 Gbp.
Last upload on 20 August 2025.
Assemblies
Individual 2 Primary Assembly
Version assembly_curated from 19 May 2025
rSteOdo2.pri.cur.20250519.fasta.gz (551.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 47.70 Mbp 1 305.34 Mbp
20 8 32.44 Mbp 2 224.23 Mbp
30 15 18.57 Mbp 2 224.23 Mbp
40 26 11.09 Mbp 4 109.76 Mbp
50 48 6.73 Mbp 5 107.61 Mbp
60 82 3.87 Mbp 7 105.33 Mbp
70 143 2.08 Mbp 9 84.63 Mbp
80 252 1.27 Mbp 11 62.78 Mbp
90 440 0.70 Mbp 16 20.53 Mbp
100 1152 3.66 Kbp 73 17.18 Kbp
1.000x 1152 1.75 Gbp 73 1.75 Gbp
NG based on genome size 1.75 Gbp.
Individual 2 Alternate Assembly
Version assembly_curated from 19 May 2025
rSteOdo2.alt.cur.20250519.fasta.gz (547.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 82.32 Mbp 1 306.56 Mbp
20 5 50.42 Mbp 2 225.59 Mbp
30 9 41.44 Mbp 2 225.59 Mbp
40 15 25.90 Mbp 4 114.60 Mbp
50 23 17.03 Mbp 5 108.35 Mbp
60 35 11.46 Mbp 7 106.96 Mbp
70 55 6.83 Mbp 8 92.89 Mbp
80 92 3.46 Mbp 11 64.12 Mbp
90 177 1.28 Mbp 15 26.14 Mbp
100 770 15.17 Kbp 217 15.17 Kbp
1.000x 770 1.76 Gbp 217 1.76 Gbp
NG based on genome size 1.75 Gbp.
Individual 2 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 2 September 2025
rSteOdo2.HiC.hap1.20250902.fasta.gz (487.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 27.75 Mbp 1 306.15 Mbp
20 13 22.32 Mbp 2 226.98 Mbp
30 21 20.63 Mbp 3 171.26 Mbp
40 30 18.16 Mbp 4 115.02 Mbp
50 42 14.33 Mbp 5 109.05 Mbp
60 57 10.31 Mbp 7 107.83 Mbp
70 77 7.71 Mbp 9 92.29 Mbp
80 106 4.75 Mbp 11 72.31 Mbp
90 164 1.98 Mbp 14 33.39 Mbp
100 640 17.40 Kbp 168 17.40 Kbp
1.000x 640 1.81 Gbp 168 1.81 Gbp
NG based on genome size 1.75 Gbp.
Individual 2 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 2 September 2025
rSteOdo2.HiC.hap2.20250902.fasta.gz (488.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 32.49 Mbp 1 308.72 Mbp
20 12 23.04 Mbp 2 226.90 Mbp
30 21 19.33 Mbp 3 212.95 Mbp
40 32 15.21 Mbp 3 212.95 Mbp
50 45 11.85 Mbp 4 171.03 Mbp
60 65 7.92 Mbp 6 108.14 Mbp
70 92 5.34 Mbp 8 106.59 Mbp
80 134 3.53 Mbp 10 86.01 Mbp
90 205 1.66 Mbp 12 63.45 Mbp
100 722 16.58 Kbp 184 16.58 Kbp
1.000x 722 1.82 Gbp 184 1.82 Gbp
NG based on genome size 1.75 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/rSteOdo2.yml (view)
species: Sternotherus odoratus
specimem: rSteOdo2
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Sternotherus_odoratus/rSteOdo2/assembly_vgp_HiC_2.0/rSteOdo2.HiC.hap1.20250902.fasta.gz
hap2: s3://genomeark/species/Sternotherus_odoratus/rSteOdo2/assembly_vgp_HiC_2.0/rSteOdo2.HiC.hap2.20250902.fasta.gz
pretext_hap1: s3://genomeark/species/Sternotherus_odoratus/rSteOdo2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/rSteOdo2_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Sternotherus_odoratus/rSteOdo2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/rSteOdo2_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Sternotherus_odoratus/rSteOdo2/assembly_vgp_HiC_2.0/evaluation/merqury/rSteOdo2_png/
pacbio_read_dir: s3://genomeark/species/Sternotherus_odoratus/rSteOdo2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Sternotherus_odoratus/rSteOdo2/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP1 genomic profiling workflow (v0.2)
  - VGP4 HiFi HiC assembly workflow (v0.3.9)
  - VGP8 HiC scaffolding workflow (v2.0)
  - VGP9 decontamination workflow (v0.7) with database PlusPF 2022
  - Pre-curation worklfow (v1.0beta6)
notes: This was a Hifiasm-HiC assembly of rSteOdo2 resulting in two haplotype assemblies. The PacBio bam files downloaded from NCBI contained CCS reads with QV <20. VGL refiltered the bam files using software extracthifi with default settings. HiC data were generated using the Arima library prep kit, and require trimming the first 5 bp off from the 5' end of both read files. The restriction enzymes used were the Arima v2 kit, so the cutting sites are GATC, GANTC, CTNAG, TTAA.
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.