Sternotherus odoratus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) rSteOdo1 90.31 Gbp N/A 73.2 GiB
Arima rSteOdo1 185.28 Gbp N/A 95.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 24 January 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rSteOdo1 PacBio HiFi (.fq) 90.31 Gbp N/A 73.2 GiB
Arima 185.28 Gbp N/A 95.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 24 January 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 14 April 2023
rSteOdo1.hap1.decon.20230414.fasta.gz (688.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 111.30 Mbp 1 481.29 Mbp
20 5 91.95 Mbp 1 481.29 Mbp
30 8 60.29 Mbp 2 307.84 Mbp
40 12 50.06 Mbp 3 304.93 Mbp
50 17 43.84 Mbp 4 256.32 Mbp
60 24 35.36 Mbp 5 221.19 Mbp
70 31 28.14 Mbp 6 138.93 Mbp
80 42 18.24 Mbp 8 88.84 Mbp
90 60 9.67 Mbp 11 76.70 Mbp
100 806 14.79 Kbp 670 14.79 Kbp
1.000x 806 2.37 Gbp 670 2.37 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 14 April 2023
rSteOdo1.hap2.cur.20230414.fasta.gz (678.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 129.54 Mbp 1 486.60 Mbp
20 5 78.28 Mbp 1 486.60 Mbp
30 8 61.35 Mbp 2 307.64 Mbp
40 12 46.78 Mbp 3 303.74 Mbp
50 18 38.56 Mbp 4 255.08 Mbp
60 25 33.13 Mbp 5 220.92 Mbp
70 32 29.12 Mbp 6 101.39 Mbp
80 42 20.35 Mbp 9 79.97 Mbp
90 59 10.06 Mbp 12 67.97 Mbp
100 355 19.50 Kbp 194 19.50 Kbp
1.000x 355 2.33 Gbp 194 2.35 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/rSteOdo1_hap2.yml (view)
species: Sternotherus odoratus specimen: rSteOdo1 projects: - vgp haplotype_to_curate: hap2 hap1: s3://genomeark/species/Sternotherus_odoratus/rSteOdo1/assembly_vgp_HiC_2.0/rSteOdo1.HiC.hap1.20230208.fasta.gz hap2: s3://genomeark/species/Sternotherus_odoratus/rSteOdo1/assembly_vgp_HiC_2.0/rSteOdo1.HiC.hap2.20230208.fasta.gz pretext_hap1: s3://genomeark/species/Sternotherus_odoratus/rSteOdo1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/rSteOdo1_hap1__s2_heatmap.pretext pretext_hap2: s3://genomeark/species/Sternotherus_odoratus/rSteOdo1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rSteOdo1_hap2__s2_heatmap.pretext kmer_spectra_img: s3://genomeark/species/Sternotherus_odoratus/rSteOdo1/assembly_vgp_HiC_2.0/evaluation/merqury/rSteOdo1_png/ pacbio_read_dir: s3://genomeark/species/Sternotherus_odoratus/rSteOdo1/genomic_data/pacbio_hifi/ pacbio_read_type: hifi bionano_cmap_dir: s3://genomeark/species/Sternotherus_odoratus/rSteOdo1/genomic_data/bionano/ hic_read_dir: s3://genomeark/species/Sternotherus_odoratus/rSteOdo1/genomic_data/arima/ pipeline: - hifiasm (0.16.1+galaxy4) - solve (3.7) - yahs (1.2a.2+galaxy0) assembled_by_group: Rockefeller notes: This was a hifiasm-HiC assembly of rSteOdo1, resulting in two complete haplotypes. This individual had bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The kmer spectra indicates a homogametic specimen. We are submitting haplotype 2 for curation. MitoHiFi was run on the raw reads, but a full mitogenome could not be recovered.
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.