Callospermophilus lateralis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mCalLat2 142.10 Gbp N/A 65.8 GiB
PacBio HiFi (.bam) mCalLat2 141.45 Gbp N/A 570.5 GiB
Arima mCalLat2 171.55 Gbp N/A 91.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 13 May 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mCalLat2 PacBio HiFi (.fq) 142.10 Gbp N/A 65.8 GiB
PacBio HiFi (.bam) 141.45 Gbp N/A 570.5 GiB
Arima 171.55 Gbp N/A 91.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 13 May 2024.
Assemblies
Individual 2 Haplotype 1 Assembly
Version assembly_curated from 13 March 2025
mCalLat2.hap1.cur.20250313.fasta.gz (1.2 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 8 50.24 Mbp 3 199.23 Mbp
20 20 31.23 Mbp 5 165.49 Mbp
30 37 21.07 Mbp 8 140.20 Mbp
40 66 13.05 Mbp 12 122.73 Mbp
50 118 6.58 Mbp 16 94.18 Mbp
60 220 3.15 Mbp 32 9.70 Mbp
70 451 1.40 Mbp 158 1.99 Mbp
80 927 0.70 Mbp 547 0.81 Mbp
90 2026 236.00 Kbp 1502 279.59 Kbp
100 9535 1 bp 8087 7.43 Kbp
1.000x 9535 4.65 Gbp 8087 4.65 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_curated from 12 March 2025
mCalLat2.hap2.cur.20250312.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 56.91 Mbp 2 210.63 Mbp
20 12 44.78 Mbp 4 177.37 Mbp
30 22 28.99 Mbp 6 160.47 Mbp
40 35 23.23 Mbp 8 136.69 Mbp
50 53 13.62 Mbp 11 114.99 Mbp
60 86 7.85 Mbp 14 93.29 Mbp
70 151 3.54 Mbp 18 63.63 Mbp
80 302 1.42 Mbp 54 3.38 Mbp
90 755 421.16 Kbp 349 0.54 Mbp
100 3463 3.72 Kbp 2820 3.72 Kbp
1.000x 3463 3.35 Gbp 2820 3.35 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/mCalLat2.yml (view)
species: Callospermophilus lateralis
specimen: mCalLat2
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Callospermophilus_lateralis/mCalLat2/assembly_vgp_HiC_2.0/mCalLat2.HiC.hap1.20240513.fasta.gz
hap2: s3://genomeark/species/Callospermophilus_lateralis/mCalLat2/assembly_vgp_HiC_2.0/mCalLat2.HiC.hap2.20240513.fasta.gz
pretext_hap1: s3://genomeark/species/Callospermophilus_lateralis/mCalLat2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mCalLat2_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Callospermophilus_lateralis/mCalLat2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mCalLat2_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Callospermophilus_lateralis/mCalLat2/assembly_vgp_HiC_2.0/evaluation/merqury/mCalLat2_png/
pacbio_read_dir: s3://genomeark/species/Callospermophilus_lateralis/mCalLat2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Callospermophilus_lateralis/mCalLat2/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - purge_dups (1.2.6+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of mCalLat2, resulting in two complete haplotypes. Hap1 underwent purging. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Arima library prep. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. 
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.