Perognathus parvus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mPerPar1 195.19 Gbp N/A 93.2 GiB
PacBio HiFi (.bam) mPerPar1 198.87 Gbp N/A 653.5 GiB
Arima mPerPar1 238.85 Gbp N/A 123.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 September 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mPerPar1 PacBio HiFi (.fq) 195.19 Gbp N/A 93.2 GiB
PacBio HiFi (.bam) 198.87 Gbp N/A 653.5 GiB
Arima 238.85 Gbp N/A 123.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 September 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 10 October 2025
mPerPar1.HiC.hap1.20251010.fasta.gz (560.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 85.98 Mbp 2 151.60 Mbp
20 6 59.82 Mbp 3 137.71 Mbp
30 10 47.54 Mbp 5 117.87 Mbp
40 14 41.98 Mbp 7 99.81 Mbp
50 20 37.69 Mbp 10 80.79 Mbp
60 26 27.30 Mbp 12 73.52 Mbp
70 35 21.20 Mbp 16 62.42 Mbp
80 49 11.57 Mbp 19 56.91 Mbp
90 78 5.04 Mbp 25 22.45 Mbp
100 447 10.04 Kbp 321 10.04 Kbp
1.000x 447 2.16 Gbp 321 2.16 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 10 October 2025
mPerPar1.HiC.hap2.20251010.fasta.gz (563.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 77.35 Mbp 2 155.25 Mbp
20 6 65.37 Mbp 3 141.37 Mbp
30 10 50.57 Mbp 5 125.60 Mbp
40 15 44.05 Mbp 7 99.91 Mbp
50 21 32.28 Mbp 10 79.75 Mbp
60 29 25.11 Mbp 12 70.72 Mbp
70 38 20.71 Mbp 16 61.84 Mbp
80 52 11.90 Mbp 19 58.39 Mbp
90 87 3.84 Mbp 24 38.53 Mbp
100 387 17.34 Kbp 249 17.34 Kbp
1.000x 387 2.20 Gbp 249 2.20 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 10 October 2025
mPerPar1.MT.20251010.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mPerPar1.yml (view)
species: Perognathus parvus
specimem: mPerPar1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Perognathus_parvus/mPerPar1/assembly_vgp_HiC_2.0/mPerPar1.HiC.hap1.20251010.fasta.gz
hap2: s3://genomeark/species/Perognathus_parvus/mPerPar1/assembly_vgp_HiC_2.0/mPerPar1.HiC.hap2.20251010.fasta.gz
pretext_hap1: s3://genomeark/species/Perognathus_parvus/mPerPar1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mPerPar1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Perognathus_parvus/mPerPar1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mPerPar1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Perognathus_parvus/mPerPar1/assembly_vgp_HiC_2.0/evaluation/merqury/mPerPar1_png/
pacbio_read_dir: s3://genomeark/species/Perognathus_parvus/mPerPar1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Perognathus_parvus/mPerPar1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.12)
  - VGP8 HiC scaffolding workflow (v2.2) with mapq=10
  - VGP9 decontamination workflow unpublished using FCS (0.5.5+galaxy0) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of mPerPar1 resulting in two haplotype assemblies. HiC data were generated using the Arima library prep kit, and require trimming the first 5 bp off from the 5' end of both read files. The restriction enzymes used were the Arima v2 kit, so the cutting sites are GATC, GANTC, CTNAG, TTAA.
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.