Ictidomys tridecemlineatus

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


No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mIctTri1 92.33 Gbp N/A 45.0 GiB
PacBio HiFi (.bam) mIctTri1 92.03 Gbp N/A 358.4 GiB
Arima mIctTri1 1021.79 Gbp N/A 486.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 4 August 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mIctTri1 PacBio HiFi (.fq) 92.33 Gbp N/A 45.0 GiB
PacBio HiFi (.bam) 92.03 Gbp N/A 358.4 GiB
Arima 1021.79 Gbp N/A 486.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 4 August 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 17 July 2025
mIctTri1.hap1.cur.20250717.fasta.gz (806.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 46.76 Mbp 2 232.66 Mbp
20 14 34.06 Mbp 3 216.62 Mbp
30 25 23.44 Mbp 5 200.60 Mbp
40 41 15.74 Mbp 6 200.30 Mbp
50 66 10.56 Mbp 8 157.08 Mbp
60 105 6.23 Mbp 10 144.91 Mbp
70 175 3.19 Mbp 12 121.93 Mbp
80 329 1.28 Mbp 15 71.68 Mbp
90 944 216.82 Kbp 244 323.22 Kbp
100 6723 7.01 Kbp 5279 7.01 Kbp
1.000x 6723 3.14 Gbp 5279 3.14 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 16 July 2025
mIctTri1.hap2.cur.20250716.fasta.gz (689.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 46.01 Mbp 2 212.68 Mbp
20 12 34.30 Mbp 3 201.18 Mbp
30 20 29.77 Mbp 4 197.37 Mbp
40 31 19.68 Mbp 5 196.55 Mbp
50 47 13.93 Mbp 7 185.36 Mbp
60 72 8.68 Mbp 8 153.80 Mbp
70 116 3.97 Mbp 10 133.50 Mbp
80 208 1.82 Mbp 12 115.94 Mbp
90 452 0.61 Mbp 16 40.59 Mbp
100 2438 4.43 Kbp 1438 9.53 Kbp
1.000x 2438 2.59 Gbp 1438 2.59 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 10 September 2024
mIctTri1.MT.20240910.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mIctTri1.yml (view)
species: Ictidomys tridecemlineatus
specimen: mIctTri1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Ictidomys_tridecemlineatus/mIctTri1/assembly_vgp_HiC_2.0/mIctTri1.HiC.hap1.20240906.fasta.gz
hap2: s3://genomeark/species/Ictidomys_tridecemlineatus/mIctTri1/assembly_vgp_HiC_2.0/mIctTri1.HiC.hap2.20240906.fasta.gz
pretext_hap1: s3://genomeark/species/Ictidomys_tridecemlineatus/mIctTri1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mIctTri1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Ictidomys_tridecemlineatus/mIctTri1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mIctTri1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Ictidomys_tridecemlineatus/mIctTri1/assembly_vgp_HiC_2.0/evaluation/merqury/mIctTri1_png/
mito: s3://genomeark/species/Ictidomys_tridecemlineatus/mIctTri1/assembly_MT_rockefeller/mIctTri1.MT.20240910.fasta.gz
pacbio_read_dir: s3://genomeark/species/Ictidomys_tridecemlineatus/mIctTri1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Ictidomys_tridecemlineatus/mIctTri1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.9+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of mIctTri1, resulting in two complete haplotypes. The HiC prep kit used was Arima, so the HiC reads require trimming 5 bp off the 5' end. The assembly was performed on the VGL Galaxy instance. 
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.