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_curated from 5 January 2026
mSagOed1.hap1.cur.20260105.fasta.gz (834.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 67.00 Mbp 2 214.80 Mbp
20 10 53.38 Mbp 4 179.30 Mbp
30 17 37.32 Mbp 5 178.98 Mbp
40 27 30.18 Mbp 7 164.38 Mbp
50 41 18.54 Mbp 9 145.55 Mbp
60 59 14.37 Mbp 12 135.32 Mbp
70 87 8.92 Mbp 14 128.36 Mbp
80 137 4.83 Mbp 17 103.25 Mbp
90 275 1.13 Mbp 22 52.30 Mbp
100 2763 3.57 Kbp 2111 13.73 Kbp
1.000x 2763 3.22 Gbp 2111 3.22 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 5 January 2026
mSagOed1.hap2.cur.20260105.fasta.gz (704.2 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 3 188.40 Mbp
30 19 27.28 Mbp 5 172.63 Mbp
40 33 14.91 Mbp 6 151.05 Mbp
50 53 10.37 Mbp 8 131.10 Mbp
60 83 7.31 Mbp 10 122.58 Mbp
70 128 4.75 Mbp 13 117.81 Mbp
80 215 2.17 Mbp 15 96.94 Mbp
90 430 0.69 Mbp 19 52.42 Mbp
100 2065 7.94 Kbp 880 13.06 Kbp
1.000x 2065 2.66 Gbp 880 2.66 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.