Zonotrichia albicollis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bZonAlb1 58.39 Gbp N/A 49.9 GiB
Arima bZonAlb1 134.39 Gbp N/A 65.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 18 July 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bZonAlb1 PacBio HiFi (.fq) 58.39 Gbp N/A 49.9 GiB
Arima 134.39 Gbp N/A 65.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 18 July 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 31 May 2024
bZonAlb1.HiC.hap1.20240531.fasta.gz (321.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 67.04 Mbp 1 157.57 Mbp
20 4 45.74 Mbp 2 120.04 Mbp
30 7 38.36 Mbp 3 118.42 Mbp
40 11 23.45 Mbp 4 74.50 Mbp
50 17 17.39 Mbp 6 64.43 Mbp
60 24 14.56 Mbp 8 42.57 Mbp
70 33 11.42 Mbp 12 23.45 Mbp
80 47 6.76 Mbp 18 15.94 Mbp
90 71 3.32 Mbp 27 9.06 Mbp
100 367 12.64 Kbp 192 12.64 Kbp
1.000x 367 1.16 Gbp 192 1.16 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 31 May 2024
bZonAlb1.HiC.hap2.20240531.fasta.gz (357.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 52.75 Mbp 1 157.84 Mbp
20 4 43.38 Mbp 2 119.34 Mbp
30 8 26.11 Mbp 3 118.17 Mbp
40 15 20.20 Mbp 5 74.75 Mbp
50 21 18.39 Mbp 7 65.41 Mbp
60 29 15.56 Mbp 9 47.02 Mbp
70 39 10.69 Mbp 13 23.92 Mbp
80 55 5.66 Mbp 19 16.66 Mbp
90 89 2.36 Mbp 31 8.50 Mbp
100 432 20.25 Kbp 174 20.25 Kbp
1.000x 432 1.30 Gbp 174 1.30 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 31 May 2024
bZonAlb1.MT.20240531.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bZonAlb1.yml (view)
species: Zonotrichia albicollis
specimen: bZonAlb1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Zonotrichia_albicollis/bZonAlb1/assembly_vgp_HiC_2.0/bZonAlb1.HiC.hap1.20240531.fasta.gz
hap2: s3://genomeark/species/Zonotrichia_albicollis/bZonAlb1/assembly_vgp_HiC_2.0/bZonAlb1.HiC.hap2.20240531.fasta.gz
pretext_hap1: s3://genomeark/species/Zonotrichia_albicollis/bZonAlb1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bZonAlb1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Zonotrichia_albicollis/bZonAlb1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bZonAlb1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Zonotrichia_albicollis/bZonAlb1/assembly_vgp_HiC_2.0/evaluation/merqury/bZonAlb1_png/
pacbio_read_dir: s3://genomeark/species/Zonotrichia_albicollis/bZonAlb1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Zonotrichia_albicollis/bZonAlb1/genomic_data/arima/
mito: s3://genomeark/species/Zonotrichia_albicollis/bZonAlb1/assembly_MT_rockefeller/bZonAlb1.MT.20240531.fasta.gz
pipeline: 
  - hifiasm (0.19.8+galaxy1)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of bZonAlb1, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Swift-IDT. The assembly was performed on usegalaxy MAIN server (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.