Ictidomys tridecemlineatus

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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 547.91 Gbp N/A 282.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 12 August 2024.
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 547.91 Gbp N/A 282.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 12 August 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 6 September 2024
mIctTri1.HiC.hap1.20240906.fasta.gz (879.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 46.76 Mbp 3 130.61 Mbp
20 14 34.06 Mbp 5 124.05 Mbp
30 25 23.44 Mbp 8 113.14 Mbp
40 42 15.68 Mbp 11 102.42 Mbp
50 67 10.56 Mbp 14 87.66 Mbp
60 105 6.23 Mbp 18 69.46 Mbp
70 176 3.17 Mbp 23 58.12 Mbp
80 335 1.23 Mbp 43 3.20 Mbp
90 1008 194.25 Kbp 461 278.05 Kbp
100 7306 7.01 Kbp 6061 7.01 Kbp
1.000x 7306 3.15 Gbp 6061 3.15 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 6 September 2024
mIctTri1.HiC.hap2.20240906.fasta.gz (750.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 46.01 Mbp 2 124.48 Mbp
20 12 34.30 Mbp 5 106.36 Mbp
30 21 28.18 Mbp 7 104.42 Mbp
40 32 19.26 Mbp 10 85.02 Mbp
50 48 13.77 Mbp 13 79.94 Mbp
60 73 8.68 Mbp 17 63.81 Mbp
70 119 3.91 Mbp 21 54.37 Mbp
80 214 1.75 Mbp 27 31.41 Mbp
90 465 0.60 Mbp 112 1.21 Mbp
100 2691 9.53 Kbp 1824 9.53 Kbp
1.000x 2691 2.61 Gbp 1824 2.61 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.