Perimyotis subflavus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mPerSub1 108.77 Gbp N/A 92.7 GiB
PacBio HiFi (.bam) mPerSub1 107.89 Gbp N/A 383.5 GiB
Arima mPerSub1 290.04 Gbp N/A 157.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 23 April 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mPerSub1 PacBio HiFi (.fq) 108.77 Gbp N/A 92.7 GiB
PacBio HiFi (.bam) 107.89 Gbp N/A 383.5 GiB
Arima 290.04 Gbp N/A 157.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 23 April 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 27 May 2026
mPerSub1.HiC.hap1.20260527.fasta.gz (588.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 95.29 Mbp 1 277.06 Mbp
20 5 81.74 Mbp 2 243.17 Mbp
30 9 67.52 Mbp 3 231.56 Mbp
40 12 58.10 Mbp 4 229.12 Mbp
50 17 50.95 Mbp 5 211.99 Mbp
60 22 38.75 Mbp 7 197.26 Mbp
70 28 32.67 Mbp 8 161.45 Mbp
80 42 9.63 Mbp 9 156.79 Mbp
90 81 3.47 Mbp 11 103.65 Mbp
100 674 20.91 Kbp 190 20.91 Kbp
1.000x 674 2.35 Gbp 190 2.35 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 27 May 2026
mPerSub1.HiC.hap2.20260527.fasta.gz (552.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 106.45 Mbp 1 345.27 Mbp
20 5 95.36 Mbp 2 244.28 Mbp
30 7 82.05 Mbp 3 228.80 Mbp
40 10 68.47 Mbp 4 219.77 Mbp
50 14 54.20 Mbp 5 211.05 Mbp
60 18 39.88 Mbp 6 201.91 Mbp
70 25 23.87 Mbp 7 157.37 Mbp
80 38 9.74 Mbp 8 154.90 Mbp
90 75 3.46 Mbp 10 133.70 Mbp
100 566 19.13 Kbp 125 19.13 Kbp
1.000x 566 2.19 Gbp 125 2.19 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 26 May 2026
mPerSub1.MT.20260526.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mPerSub1.yml (view)
species: Perimyotis subflavus
specimen: mPerSub1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Perimyotis_subflavus/mPerSub1/assembly_vgp_HiC_2.0/mPerSub1.HiC.hap1.20260527.fasta.gz
hap2: s3://genomeark/species/Perimyotis_subflavus/mPerSub1/assembly_vgp_HiC_2.0/mPerSub1.HiC.hap2.20260527.fasta.gz
pretext_hap1: s3://genomeark/species/Perimyotis_subflavus/mPerSub1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mPerSub1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Perimyotis_subflavus/mPerSub1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mPerSub1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Perimyotis_subflavus/mPerSub1/assembly_vgp_HiC_2.0/evaluation/merqury/mPerSub1_png/
pacbio_read_dir: s3://genomeark/species/Perimyotis_subflavus/mPerSub1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Perimyotis_subflavus/mPerSub1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy3)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.9)
  - VGP4 HiFi HiC assembly workflow (v0.6)
  - VGP8 HiC scaffolding workflow (v3.5) with mapq=10
  - VGP9 decontamination workflow (v1.3)
  - Pre-curation workflow (v2.4) with mapq=10, keep HiC duplicates and generate high-resolution map
notes: This was a Hifiasm-HiC assembly of mPerSub1 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.