Vicugna pacos

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) mVicPac1 481.09 Gbp N/A 838.7 GiB
PacBio HiFi (.fq) mVicPac1 119.53 Gbp N/A 64.3 GiB
PacBio HiFi (.bam) mVicPac1 816.31 Gbp N/A 393.2 GiB
Dovetail Genomics mVicPac1 247.72 Gbp N/A 140.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 19 March 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mVicPac1 PacBio HiFi (subreads) 481.09 Gbp N/A 838.7 GiB
PacBio HiFi (.fq) 119.53 Gbp N/A 64.3 GiB
PacBio HiFi (.bam) 816.31 Gbp N/A 393.2 GiB
Dovetail Genomics 247.72 Gbp N/A 140.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 19 March 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 13 June 2024
mVicPac1.HiC.hap1.20240613.fasta.gz (715.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 100.51 Mbp 3 119.75 Mbp
20 6 76.62 Mbp 5 100.02 Mbp
30 9 64.98 Mbp 8 84.43 Mbp
40 14 42.78 Mbp 11 76.62 Mbp
50 22 29.31 Mbp 15 65.69 Mbp
60 32 23.01 Mbp 20 42.78 Mbp
70 46 14.88 Mbp 28 28.82 Mbp
80 78 6.01 Mbp 42 9.27 Mbp
90 142 2.51 Mbp 95 3.23 Mbp
100 872 9.53 Kbp 812 9.53 Kbp
1.000x 872 2.68 Gbp 812 2.68 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 13 June 2024
mVicPac1.HiC.hap2.20240613.fasta.gz (635.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 100.48 Mbp 2 121.15 Mbp
20 5 78.96 Mbp 4 97.41 Mbp
30 8 65.81 Mbp 7 85.36 Mbp
40 12 58.11 Mbp 10 77.28 Mbp
50 18 32.87 Mbp 13 68.62 Mbp
60 25 26.91 Mbp 17 53.37 Mbp
70 36 18.05 Mbp 22 36.79 Mbp
80 53 9.51 Mbp 30 24.65 Mbp
90 95 3.28 Mbp 54 4.33 Mbp
100 617 15.96 Kbp 546 15.96 Kbp
1.000x 617 2.30 Gbp 546 2.30 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/mVicPac1.yml (view)
species: Vicugna pacos
specimen: mVicPac1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Vicugna_pacos/mVicPac1/assembly_vgp_HiC_2.0/mVicPac1.HiC.hap1.20240613.fasta.gz
hap2: s3://genomeark/species/Vicugna_pacos/mVicPac1/assembly_vgp_HiC_2.0/mVicPac1.HiC.hap2.20240613.fasta.gz
pretext_hap1: s3://genomeark/species/Vicugna_pacos/mVicPac1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mVicPac1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Vicugna_pacos/mVicPac1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mVicPac1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Vicugna_pacos/mVicPac1/assembly_vgp_HiC_2.0/evaluation/merqury/hap1_purged/mVicPac1_png/
pacbio_read_dir: s3://genomeark/species/Vicugna_pacos/mVicPac1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Vicugna_pacos/mVicPac1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Vicugna_pacos/mVicPac1/genomic_data/dovetail/
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.1)
notes: This was a Hifiasm-HiC assembly of mVicPac1, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Dovetail. The contigging took place on the RU Galaxy server, while the scaffolding was done via command line due to a problem with one of the conda packages needed for the Galaxy run.
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.