Macaca nemestrina

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mMacNem1 119.73 Gbp N/A 81.5 GiB
Arima mMacNem1 274.49 Gbp N/A 144.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 21 June 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mMacNem1 PacBio HiFi (.fq) 119.73 Gbp N/A 81.5 GiB
Arima 274.49 Gbp N/A 144.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 21 June 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 10 July 2023
mMacNem1.HiC.hap1.20230710.fasta.gz (809.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 96.20 Mbp 2 203.90 Mbp
20 7 76.18 Mbp 3 193.70 Mbp
30 11 64.21 Mbp 5 178.88 Mbp
40 16 51.75 Mbp 7 175.73 Mbp
50 22 40.84 Mbp 8 143.91 Mbp
60 31 30.66 Mbp 11 132.76 Mbp
70 42 23.41 Mbp 13 123.06 Mbp
80 59 14.06 Mbp 16 94.85 Mbp
90 92 6.09 Mbp 19 68.62 Mbp
100 571 12.48 Kbp 392 12.48 Kbp
1.000x 571 2.95 Gbp 392 2.95 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 10 July 2023
mMacNem1.HiC.hap2.20230710.fasta.gz (857.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 78.03 Mbp 2 198.82 Mbp
20 8 65.33 Mbp 4 198.03 Mbp
30 13 55.51 Mbp 5 189.33 Mbp
40 19 48.27 Mbp 7 172.63 Mbp
50 27 32.87 Mbp 9 142.26 Mbp
60 38 25.83 Mbp 11 135.21 Mbp
70 51 20.71 Mbp 14 115.23 Mbp
80 70 13.52 Mbp 17 95.73 Mbp
90 105 5.64 Mbp 20 81.87 Mbp
100 487 13.59 Kbp 300 13.59 Kbp
1.000x 487 3.14 Gbp 300 3.14 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.