Rhineura floridana

Florida worm lizard

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank rRhiFlo1: GCA_030035675.1 rRhiFlo1: GCA_030035715.1
ENA rRhiFlo1: GCA_030035675.1 rRhiFlo1: GCA_030035715.1
UCSC Genome Browser rRhiFlo1: GCA_030035675.1 rRhiFlo1: GCA_030035715.1

metadata.yaml (view) (edit on github)
species:
  name: Rhineura floridana
  individuals:
  - short_name: rRhiFlo1
  short_name: rRhiFlo
  taxon_id: 261503
  common_name: Florida worm lizard
  genome_size: 1623000000
  genome_size_method: GoAT
  order:
    name: Squamata
  family:
    name: Rhineuridae
  project: [ vgp ]
CC BY-NC-SA 2.0 Mary Keim (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) rRhiFlo1 62.24 Gbp 38.35x 47.5 GiB
Bionano rRhiFlo1 N/A 204.64x 545.2 MiB
Arima rRhiFlo1 209.96 Gbp 129.36x 97.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.62 Gbp.
Last upload on 24 February 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rRhiFlo1 PacBio HiFi (.fq) 62.24 Gbp 38.35x 47.5 GiB
Bionano N/A 204.64x 545.2 MiB
Arima 209.96 Gbp 129.36x 97.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.62 Gbp.
Last upload on 24 February 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 6 April 2023
rRhiFlo1.hap1.decon.20230406.fasta.gz (673.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 65.19 Mbp 1 323.94 Mbp
20 6 38.31 Mbp 2 239.81 Mbp
30 11 28.38 Mbp 2 239.81 Mbp
40 17 25.31 Mbp 3 232.59 Mbp
50 24 23.72 Mbp 4 212.30 Mbp
60 31 19.21 Mbp 4 212.30 Mbp
70 40 16.77 Mbp 5 194.48 Mbp
80 51 14.82 Mbp 6 188.58 Mbp
90 62 12.98 Mbp 7 158.20 Mbp
100 75 11.65 Mbp 8 155.10 Mbp
1.428x 836 2.32 Gbp 623 2.32 Gbp
NG based on genome size 1.62 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 6 April 2023
rRhiFlo1.hap2.cur.20230406.fasta.gz (668.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 59.66 Mbp 1 323.58 Mbp
20 6 40.35 Mbp 2 240.32 Mbp
30 10 36.08 Mbp 2 240.32 Mbp
40 15 30.06 Mbp 3 232.43 Mbp
50 22 24.20 Mbp 4 211.90 Mbp
60 29 21.77 Mbp 4 211.90 Mbp
70 37 18.40 Mbp 5 188.68 Mbp
80 46 15.52 Mbp 6 158.44 Mbp
90 57 13.98 Mbp 7 155.51 Mbp
100 70 10.48 Mbp 8 136.23 Mbp
1.418x 318 2.30 Gbp 76 2.31 Gbp
NG based on genome size 1.62 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 6 March 2023
rRhiFlo1.MT.20230306.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/rRhiFlo1_hap2.yml (view)
species: Rhineura floridana
specimen: rRhiFlo1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Rhineura_floridana/rRhiFlo1/assembly_vgp_HiC_2.0/rRhiFlo1.HiC.hap1.20230305.fasta.gz
hap2: s3://genomeark/species/Rhineura_floridana/rRhiFlo1/assembly_vgp_HiC_2.0/rRhiFlo1.HiC.hap2.20230305.fasta.gz
pretext_hap1: s3://genomeark/species/Rhineura_floridana/rRhiFlo1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/rRhiFlo1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Rhineura_floridana/rRhiFlo1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rRhiFlo1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Rhineura_floridana/rRhiFlo1/assembly_vgp_HiC_2.0/evaluation/merqury/rRhiFlo1_png/
mito: s3://genomeark/working/temp_mitos/rRhiFlo1.MT.20230306.fasta.gz
pacbio_read_dir: s3://genomeark/species/Rhineura_floridana/rRhiFlo1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Rhineura_floridana/rRhiFlo1/genomic_data/arima/
bionano_cmap_dir: s3://genomeark/species/Rhineura_floridana/rRhiFlo1/genomic_data/bionano/
pipeline:
  - hifiasm (0.18.5+galaxy1)
  - solve (3.7)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of rRhiFlo1, resulting in two complete haplotypes. This individual had bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. We are submitting hap2 for curation.
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.