Babyrousa celebensis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mBabCel1 77.17 Gbp N/A 33.6 GiB
PacBio HiFi (.bam) mBabCel1 77.45 Gbp N/A 313.3 GiB
Arima mBabCel1 220.68 Gbp N/A 120.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 29 July 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mBabCel1 PacBio HiFi (.fq) 77.17 Gbp N/A 33.6 GiB
PacBio HiFi (.bam) 77.45 Gbp N/A 313.3 GiB
Arima 220.68 Gbp N/A 120.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 29 July 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 12 August 2024
mBabCel1.HiC.hap1.20240812.fasta.gz (654.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 49.45 Mbp 1 283.35 Mbp
20 10 34.39 Mbp 2 267.68 Mbp
30 17 25.83 Mbp 3 197.83 Mbp
40 28 18.75 Mbp 5 137.63 Mbp
50 42 13.22 Mbp 6 131.32 Mbp
60 63 9.04 Mbp 8 115.31 Mbp
70 93 6.05 Mbp 11 92.67 Mbp
80 149 3.06 Mbp 13 78.85 Mbp
90 268 1.15 Mbp 18 44.16 Mbp
100 2342 3.14 Kbp 1799 3.14 Kbp
1.000x 2342 2.29 Gbp 1799 2.29 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 12 August 2024
mBabCel1.HiC.hap2.20240812.fasta.gz (722.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 38.80 Mbp 1 287.03 Mbp
20 12 30.70 Mbp 2 274.97 Mbp
30 21 25.79 Mbp 4 154.13 Mbp
40 34 18.18 Mbp 5 143.05 Mbp
50 51 12.46 Mbp 7 134.14 Mbp
60 74 9.30 Mbp 9 125.93 Mbp
70 108 5.77 Mbp 11 106.38 Mbp
80 168 3.24 Mbp 14 78.60 Mbp
90 297 1.11 Mbp 19 42.67 Mbp
100 3188 4.98 Kbp 2689 4.98 Kbp
1.000x 3188 2.58 Gbp 2689 2.58 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 12 August 2024
mBabCel1.MT.20240812.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mBabCel1.yml (view)
species: Babyrousa celebensis
specimen: mBabCel1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Babyrousa_celebensis/mBabCel1/assembly_vgp_HiC_2.0/mBabCel1.HiC.hap1.20240708.fasta.gz
hap2: s3://genomeark/species/Babyrousa_celebensis/mBabCel1/assembly_vgp_HiC_2.0/mBabCel1.HiC.hap2.20240708.fasta.gz
pretext_hap1: s3://genomeark/species/Babyrousa_celebensis/mBabCel1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mBabCel1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Babyrousa_celebensis/mBabCel1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mBabCel1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Babyrousa_celebensis/mBabCel1/assembly_vgp_HiC_2.0/evaluation/merqury/mBabCel1_png/
mito: s3://genomeark/species/Babyrousa_celebensis/mBabCel1/assembly_MT_rockefeller/mBabCel1.MT.20240812.fasta.gz
pacbio_read_dir: s3://genomeark/species/Babyrousa_celebensis/mBabCel1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Babyrousa_celebensis/mBabCel1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.8+galaxy1)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of mBabCel1, resulting in two complete haplotypes. The HiC prep kit used was Arima, so the HiC reads require trimming 5 bp off the 5' end. The assembly was performed on vgp.usegalaxy.org. 
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.