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 776.26 Gbp N/A 636.1 GiB
Dovetail Genomics mVicPac1 123.86 Gbp N/A 70.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 27 March 2026.
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) 776.26 Gbp N/A 636.1 GiB
Dovetail Genomics 123.86 Gbp N/A 70.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 27 March 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 10 March 2026
mVicPac1.hap1.cur.20260310.fasta.gz (717.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 100.51 Mbp 3 121.45 Mbp
20 6 76.62 Mbp 5 106.85 Mbp
30 10 64.98 Mbp 7 96.13 Mbp
40 15 39.58 Mbp 11 79.13 Mbp
50 23 28.46 Mbp 14 68.79 Mbp
60 33 22.51 Mbp 19 53.65 Mbp
70 47 14.73 Mbp 24 42.46 Mbp
80 77 6.06 Mbp 32 30.83 Mbp
90 141 2.54 Mbp 57 4.63 Mbp
100 863 1.08 Kbp 722 9.53 Kbp
1.000x 863 2.69 Gbp 722 2.69 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 10 March 2026
mVicPac1.hap2.cur.20260310.fasta.gz (578.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 107.90 Mbp 2 121.21 Mbp
20 5 78.58 Mbp 4 100.02 Mbp
30 8 65.10 Mbp 7 86.42 Mbp
40 12 58.11 Mbp 9 81.34 Mbp
50 17 34.81 Mbp 13 69.62 Mbp
60 25 28.07 Mbp 16 61.66 Mbp
70 35 18.05 Mbp 20 43.39 Mbp
80 53 7.74 Mbp 27 30.57 Mbp
90 96 3.26 Mbp 36 8.26 Mbp
100 607 7.87 Kbp 475 17.97 Kbp
1.000x 607 2.28 Gbp 475 2.28 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.