Macaca nemestrina

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) mMacNem1 2309.88 Gbp N/A 3.9 TiB
PacBio HiFi (.fq) mMacNem1 119.73 Gbp N/A 81.5 GiB
PacBio HiFi (.bam) mMacNem1 358.60 Gbp N/A 1.2 TiB
Arima mMacNem1 274.49 Gbp N/A 144.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 8 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mMacNem1 PacBio HiFi (subreads) 2309.88 Gbp N/A 3.9 TiB
PacBio HiFi (.fq) 119.73 Gbp N/A 81.5 GiB
PacBio HiFi (.bam) 358.60 Gbp N/A 1.2 TiB
Arima 274.49 Gbp N/A 144.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 8 June 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 10 June 2024
mMacNem1.hap1.cur.20240610.fasta.gz (854.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 96.11 Mbp 2 203.90 Mbp
20 7 76.18 Mbp 3 192.02 Mbp
30 12 58.47 Mbp 5 184.15 Mbp
40 17 50.33 Mbp 7 179.31 Mbp
50 24 40.84 Mbp 9 154.80 Mbp
60 33 30.66 Mbp 11 143.91 Mbp
70 45 20.83 Mbp 13 134.12 Mbp
80 64 13.43 Mbp 16 118.47 Mbp
90 101 5.50 Mbp 19 88.96 Mbp
100 621 11.87 Kbp 361 12.48 Kbp
1.000x 621 3.12 Gbp 361 3.12 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 10 June 2024
mMacNem1.hap2.cur.20240610.fasta.gz (811.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 85.10 Mbp 2 203.96 Mbp
20 7 70.37 Mbp 3 200.63 Mbp
30 12 57.03 Mbp 5 189.72 Mbp
40 18 47.29 Mbp 6 184.88 Mbp
50 26 31.52 Mbp 8 152.80 Mbp
60 36 25.83 Mbp 10 142.26 Mbp
70 48 20.86 Mbp 12 134.65 Mbp
80 66 13.52 Mbp 15 120.75 Mbp
90 97 6.06 Mbp 17 91.01 Mbp
100 465 13.59 Kbp 233 13.59 Kbp
1.000x 465 2.96 Gbp 233 2.96 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 10 July 2023
mMacNem1.MT.20230710.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mMacNem1.yml (view)
species: Macaca nemestrina
specimen: mMacNem1
projects: 
  - vgp
hap1: s3://genomeark/species/Macaca_nemestrina/mMacNem1/assembly_vgp_HiC_2.0/mMacNem1.HiC.hap1.20230710.fasta.gz
hap2: s3://genomeark/species/Macaca_nemestrina/mMacNem1/assembly_vgp_HiC_2.0/mMacNem1.HiC.hap2.20230710.fasta.gz
pretext_hap1: s3://genomeark/species/Macaca_nemestrina/mMacNem1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mMacNem1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Macaca_nemestrina/mMacNem1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mMacNem1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Macaca_nemestrina/mMacNem1/assembly_vgp_HiC_2.0/evaluation/merqury/mMacNem1_png/
mito: s3://genomeark/species/Macaca_nemestrina/mMacNem1/assembly_MT_rockefeller/mMacNem1.MT.20230710.fasta.gz
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of mMacNem1, resulting in two complete haplotypes. This individual did not bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit.
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.