Saimiri boliviensis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mSaiBol1 95.64 Gbp 34.81x 48.0 GiB
PacBio HiFi (.bam) mSaiBol1 1290.98 Gbp 469.88x 639.9 GiB
Arima mSaiBol1 5.98 Gbp 2.17x 3.3 GiB
mSaiBol2 146.21 Gbp 53.22x 77.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.75 Gbp.
Last upload on 14 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mSaiBol1 PacBio HiFi (.fq) 95.64 Gbp 34.81x 48.0 GiB
PacBio HiFi (.bam) 1290.98 Gbp 469.88x 639.9 GiB
Arima 5.98 Gbp 2.17x 3.3 GiB
mSaiBol2 Arima 146.21 Gbp 53.22x 77.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.75 Gbp.
Last upload on 14 June 2024.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 11 February 2025
mSaiBol1.pri.cur.20250211.fasta.gz (720.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 160.79 Mbp 1 302.01 Mbp
20 4 119.90 Mbp 3 181.10 Mbp
30 7 106.70 Mbp 4 167.61 Mbp
40 9 103.83 Mbp 6 137.54 Mbp
50 13 69.22 Mbp 8 129.41 Mbp
60 18 47.22 Mbp 10 127.52 Mbp
70 24 41.85 Mbp 12 123.85 Mbp
80 32 28.66 Mbp 15 95.95 Mbp
90 43 19.84 Mbp 18 72.67 Mbp
100 135 20.54 Kbp 62 20.84 Kbp
1.000x 135 2.75 Gbp 62 2.75 Gbp
NG based on genome size 2.75 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 11 February 2025
mSaiBol1.alt.cur.20250211.fasta.gz (744.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 89 1.09 Mbp 85 1.10 Mbp
20 437 0.67 Mbp 433 0.67 Mbp
30 944 497.45 Kbp 940 497.45 Kbp
40 1612 381.94 Kbp 1608 381.94 Kbp
50 2487 287.31 Kbp 2483 287.31 Kbp
60 3662 210.75 Kbp 3657 210.86 Kbp
70 5315 145.52 Kbp 5310 145.57 Kbp
80 7843 90.11 Kbp 7838 90.11 Kbp
90 12228 49.56 Kbp 12223 49.56 Kbp
100 21333 6.98 Kbp 21328 6.98 Kbp
1.000x 21333 2.90 Gbp 21328 2.90 Gbp
NG based on genome size 2.75 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 2 September 2024
mSaiBol1.MT.20240902.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_standard_2.0/mSaiBol1.yml (view)
species: Saimiri boliviensis
specimen: mSaiBol1
projects: 
  - vgp
data_location: S3
release_to: S3
primary: s3://genomeark/species/Saimiri_boliviensis/mSaiBol1/assembly_vgp_standard_2.0/mSaiBol1.standard.pri.20240902.fasta.gz
haplotigs: s3://genomeark/species/Saimiri_boliviensis/mSaiBol1/assembly_vgp_standard_2.0/mSaiBol1.standard.alt.20240902.fasta.gz
pretext: s3://genomeark/species/Saimiri_boliviensis/mSaiBol1/assembly_vgp_standard_2.0/evaluation/pri/pretext/mSaiBol1_pri__s2.heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Saimiri_boliviensis/mSaiBol1/assembly_vgp_standard_2.0/evaluation/merqury/mSaiBol1_png/
mito: s3://genomeark/species/Saimiri_boliviensis/mSaiBol1/assembly_MT_rockefeller/mSaiBol1.MT.20240902.fasta.gz
pacbio_read_dir: s3://genomeark/species/Saimiri_boliviensis/mSaiBol1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Saimiri_boliviensis/mSaiBol2/genomic_data/arima/
pipeline:
  - hifiasm (0.18.8+galaxy1)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a primary/alternate assembly of mSaiBol1. The HiC prep was Arima kit 2. HiC data came from a different individual (mSaiBol2) than the HiFi data (mSaiBol1). The primary contigs did not look like they needed purging, so purge_dups was not run on this assembly. HiC coverage was lower than usual (~45X).
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.