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_vgp_HiC_2.0 from 13 May 2024
mCalLat2.HiC.hap1.20240513.fasta.gz (1.2 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 7 53.24 Mbp 3 161.39 Mbp
20 19 32.22 Mbp 6 133.72 Mbp
30 36 21.53 Mbp 10 113.85 Mbp
40 64 13.13 Mbp 14 85.28 Mbp
50 116 6.58 Mbp 21 63.53 Mbp
60 218 3.15 Mbp 54 6.37 Mbp
70 451 1.39 Mbp 200 1.80 Mbp
80 937 0.69 Mbp 607 0.79 Mbp
90 2092 219.12 Kbp 1609 261.97 Kbp
100 10196 7.43 Kbp 8807 7.43 Kbp
1.000x 10196 4.68 Gbp 8807 4.68 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 13 May 2024
mCalLat2.HiC.hap2.20240513.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 51.37 Mbp 3 149.48 Mbp
20 13 38.72 Mbp 5 132.47 Mbp
30 23 28.21 Mbp 8 112.95 Mbp
40 36 21.39 Mbp 11 89.56 Mbp
50 56 13.21 Mbp 15 74.69 Mbp
60 90 7.60 Mbp 20 62.33 Mbp
70 159 3.47 Mbp 30 14.96 Mbp
80 319 1.34 Mbp 89 2.41 Mbp
90 806 388.97 Kbp 442 474.34 Kbp
100 4094 3.72 Kbp 3515 3.72 Kbp
1.000x 4094 3.36 Gbp 3515 3.36 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.