Saguinus oedipus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mSagOed1 122.94 Gbp N/A 58.6 GiB
PacBio HiFi (.bam) mSagOed1 123.75 Gbp N/A 404.5 GiB
Arima mSagOed1 344.51 Gbp N/A 182.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 23 April 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mSagOed1 PacBio HiFi (.fq) 122.94 Gbp N/A 58.6 GiB
PacBio HiFi (.bam) 123.75 Gbp N/A 404.5 GiB
Arima 344.51 Gbp N/A 182.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 23 April 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 15 September 2025
mSagOed1.HiC.hap1.20250915.fasta.gz (833.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 67.00 Mbp 2 214.08 Mbp
20 10 53.38 Mbp 4 178.98 Mbp
30 17 37.32 Mbp 5 170.79 Mbp
40 27 30.18 Mbp 7 164.38 Mbp
50 41 18.54 Mbp 10 140.94 Mbp
60 60 14.27 Mbp 12 134.68 Mbp
70 88 8.77 Mbp 14 129.09 Mbp
80 139 4.78 Mbp 17 103.73 Mbp
90 287 1.03 Mbp 21 53.94 Mbp
100 3510 13.73 Kbp 2918 13.73 Kbp
1.000x 3510 3.23 Gbp 2918 3.23 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 15 September 2025
mSagOed1.HiC.hap2.20250915.fasta.gz (710.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 50.80 Mbp 2 188.98 Mbp
20 11 36.03 Mbp 3 182.68 Mbp
30 20 25.01 Mbp 5 169.99 Mbp
40 33 14.91 Mbp 7 129.88 Mbp
50 55 10.26 Mbp 9 122.04 Mbp
60 86 7.22 Mbp 11 116.22 Mbp
70 133 4.27 Mbp 13 114.29 Mbp
80 225 2.07 Mbp 16 77.97 Mbp
90 465 0.63 Mbp 21 34.93 Mbp
100 2615 13.06 Kbp 1498 13.06 Kbp
1.000x 2615 2.70 Gbp 1498 2.70 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/mSagOed1.yml (view)
species: Saguinus oedipus
specimem: mSagOed1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Saguinus_oedipus/mSagOed1/assembly_vgp_HiC_2.0/mSagOed1.HiC.hap1.20250915.fasta.gz
hap2: s3://genomeark/species/Saguinus_oedipus/mSagOed1/assembly_vgp_HiC_2.0/mSagOed1.HiC.hap2.20250915.fasta.gz
pretext_hap1: s3://genomeark/species/Saguinus_oedipus/mSagOed1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mSagOed1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Saguinus_oedipus/mSagOed1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mSagOed1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Saguinus_oedipus/mSagOed1/assembly_vgp_HiC_2.0/evaluation/merqury/mSagOed1_png/
pacbio_read_dir: s3://genomeark/species/Saguinus_oedipus/mSagOed1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Saguinus_oedipus/mSagOed1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.11)
  - VGP8 HiC scaffolding workflow (v2.2) mapq=10
  - VGP9 decontamination workflow (v0.7) with database PlusPF 2022
  - Pre-curation worklfow (v1.0beta6) mapq=10
notes: This was a Hifiasm-HiC assembly of mSagOed1 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. I did not assemble the mitogenome because mitoHiFi is taking unusually long and unusual amounts of memory. The decontamination step removed a lot of mitochondrial scaffolds, indicating something is going on in the reads...
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.