Leontopithecus rosalia

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mLeoRos1 120.70 Gbp N/A 55.7 GiB
PacBio HiFi (.bam) mLeoRos1 122.07 Gbp N/A 393.2 GiB
Arima mLeoRos1 240.45 Gbp N/A 124.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 24 June 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mLeoRos1 PacBio HiFi (.fq) 120.70 Gbp N/A 55.7 GiB
PacBio HiFi (.bam) 122.07 Gbp N/A 393.2 GiB
Arima 240.45 Gbp N/A 124.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 24 June 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 18 September 2025
mLeoRos1.HiC.hap1.20250918.fasta.gz (749.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 120.31 Mbp 2 193.56 Mbp
20 5 103.39 Mbp 3 191.13 Mbp
30 8 86.27 Mbp 5 167.12 Mbp
40 12 70.82 Mbp 7 156.04 Mbp
50 16 54.10 Mbp 9 140.31 Mbp
60 22 43.60 Mbp 11 127.39 Mbp
70 31 22.61 Mbp 13 121.18 Mbp
80 49 10.01 Mbp 16 98.00 Mbp
90 105 2.67 Mbp 20 43.05 Mbp
100 811 13.66 Kbp 536 13.66 Kbp
1.000x 811 2.87 Gbp 536 2.87 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 18 September 2025
mLeoRos1.HiC.hap2.20250918.fasta.gz (820.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 128.99 Mbp 2 206.56 Mbp
20 5 119.81 Mbp 4 184.01 Mbp
30 9 80.73 Mbp 5 167.56 Mbp
40 13 59.39 Mbp 7 164.46 Mbp
50 19 45.71 Mbp 9 143.41 Mbp
60 26 35.94 Mbp 12 134.06 Mbp
70 37 25.76 Mbp 14 123.30 Mbp
80 53 13.33 Mbp 17 102.38 Mbp
90 89 5.80 Mbp 22 47.99 Mbp
100 471 14.68 Kbp 332 14.68 Kbp
1.000x 471 3.18 Gbp 332 3.18 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 18 September 2025
mLeoRos1.MT.20250918.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mLeoRos1.yml (view)
species: Leontopithecus rosalia
specimem: mLeoRos1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Leontopithecus_rosalia/mLeoRos1/assembly_vgp_HiC_2.0/mLeoRos1.HiC.hap1.20250918.fasta.gz
hap2: s3://genomeark/species/Leontopithecus_rosalia/mLeoRos1/assembly_vgp_HiC_2.0/mLeoRos1.HiC.hap2.20250918.fasta.gz
pretext_hap1: s3://genomeark/species/Leontopithecus_rosalia/mLeoRos1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mLeoRos1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Leontopithecus_rosalia/mLeoRos1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mLeoRos1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Leontopithecus_rosalia/mLeoRos1/assembly_vgp_HiC_2.0/evaluation/merqury/mLeoRos1_png/
pacbio_read_dir: s3://genomeark/species/Leontopithecus_rosalia/mLeoRos1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Leontopithecus_rosalia/mLeoRos1/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 (v0.7) with database PlusPF 2022
  - Pre-curation worklfow (v1.0beta6) with mapq=20
notes: This was a Hifiasm-HiC assembly of mLeoRos1 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.