Thomomys bottae

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


Resource Primary Assembly Alternate Assembly
GenBank mThoBot1: GCA_024803745.1 mThoBot1: GCA_024803775.1
ENA mThoBot1: GCA_024803745.1 mThoBot1: GCA_024803775.1
UCSC Genome Browser mThoBot1: GCA_024803745.1 mThoBot1: GCA_024803775.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mThoBot2 137.75 Gbp N/A 102.0 GiB
Arima mThoBot2 354.49 Gbp N/A 173.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 14 March 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mThoBot2 PacBio HiFi (.fq) 137.75 Gbp N/A 102.0 GiB
Arima 354.49 Gbp N/A 173.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 14 March 2023.
Assemblies
Individual 2 Haplotype 1 Assembly
Version assembly_curated from 1 August 2023
mThoBot2.hap1.cur.20230801.fasta.gz (571.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 10 15.77 Mbp 2 106.04 Mbp
20 26 10.88 Mbp 5 86.34 Mbp
30 46 9.06 Mbp 7 84.78 Mbp
40 71 7.36 Mbp 9 71.53 Mbp
50 102 5.92 Mbp 12 64.42 Mbp
60 140 4.57 Mbp 16 59.48 Mbp
70 192 3.23 Mbp 20 48.60 Mbp
80 269 2.00 Mbp 25 28.37 Mbp
90 409 0.93 Mbp 36 7.95 Mbp
100 1401 11.06 Kbp 626 11.06 Kbp
1.000x 1401 2.02 Gbp 626 2.02 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_curated from 1 August 2023
mThoBot2.hap2.cur.20230801.fasta.gz (533.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 10 16.18 Mbp 2 102.36 Mbp
20 23 11.73 Mbp 4 86.10 Mbp
30 42 8.82 Mbp 7 82.32 Mbp
40 64 7.61 Mbp 9 69.54 Mbp
50 92 6.18 Mbp 12 61.33 Mbp
60 126 4.78 Mbp 15 59.15 Mbp
70 170 3.73 Mbp 18 50.19 Mbp
80 230 2.56 Mbp 23 31.63 Mbp
90 329 1.24 Mbp 32 11.83 Mbp
100 878 14.78 Kbp 337 14.78 Kbp
1.000x 878 1.87 Gbp 337 1.87 Gbp
NG based on genome size .
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 4 May 2023
mThoBot2.MT.20230504.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mThoBot2_hap1.yml (view)
species: Thomomys bottae
specimen: mThoBot2
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Thomomys_bottae/mThoBot2/assembly_vgp_HiC_2.0/mThoBot2.HiC.hap1.20230503.fasta.gz
hap2: s3://genomeark/species/Thomomys_bottae/mThoBot2/assembly_vgp_HiC_2.0/mThoBot2.HiC.hap2.20230503.fasta.gz
pretext_hap1: s3://genomeark/species/Thomomys_bottae/mThoBot2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mThoBot2_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Thomomys_bottae/mThoBot2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mThoBot2_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Thomomys_bottae/mThoBot2/assembly_vgp_HiC_2.0/evaluation/merqury_postpurge/mThoBot2_png/
mito: s3://genomeark/species/Thomomys_bottae/mThoBot2/assembly_MT_rockefeller/mThoBot2.MT.20230504.fasta.gz
mito_gb: s3://genomeark/species/Thomomys_bottae/mThoBot2/assembly_MT_rockefeller/mThoBot2.MT.20230504.gb
pacbio_read_dir: s3://genomeark/species/Thomomys_bottae/mThoBot2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Thomomys_bottae/mThoBot2/genomic_data/arima/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - purge_dups (1.2.6+galaxy0)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of mThoBot2, 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. 
assembly_vgp_HiC_2.0/mThoBot2_hap2.yml (view)
species: Thomomys bottae
specimen: mThoBot2
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Thomomys_bottae/mThoBot2/assembly_vgp_HiC_2.0/mThoBot2.HiC.hap1.20230503.fasta.gz
hap2: s3://genomeark/species/Thomomys_bottae/mThoBot2/assembly_vgp_HiC_2.0/mThoBot2.HiC.hap2.20230503.fasta.gz
pretext_hap1: s3://genomeark/species/Thomomys_bottae/mThoBot2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mThoBot2_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Thomomys_bottae/mThoBot2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mThoBot2_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Thomomys_bottae/mThoBot2/assembly_vgp_HiC_2.0/evaluation/merqury_postpurge/mThoBot2_png/
mito: s3://genomeark/species/Thomomys_bottae/mThoBot2/assembly_MT_rockefeller/mThoBot2.MT.20230504.fasta.gz
mito_gb: s3://genomeark/species/Thomomys_bottae/mThoBot2/assembly_MT_rockefeller/mThoBot2.MT.20230504.gb
pacbio_read_dir: s3://genomeark/species/Thomomys_bottae/mThoBot2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Thomomys_bottae/mThoBot2/genomic_data/arima/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - purge_dups (1.2.6+galaxy0)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of mThoBot2, 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. 
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.