Zonotrichia albicollis

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Resource Primary Assembly Alternate Assembly
GenBank bZonAlb1: GCA_047774235.1 bZonAlb1: GCA_047830755.1 bZonAlb2: GCA_052095285.1 bZonAlb2: GCA_052095305.1
ENA bZonAlb1: GCA_047774235.1 bZonAlb1: GCA_047830755.1 bZonAlb2: GCA_052095285.1 bZonAlb2: GCA_052095305.1
UCSC Genome Browser bZonAlb1: GCA_047774235.1 bZonAlb1: GCA_047830755.1 bZonAlb2: GCA_052095285.1 bZonAlb2: GCA_052095305.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bZonAlb1 1185.51 Gbp N/A 2.0 TiB
PacBio HiFi (.fq) bZonAlb1 58.39 Gbp N/A 49.9 GiB
bZonAlb3 79.97 Gbp N/A 39.0 GiB
PacBio HiFi (.bam) bZonAlb1 178.89 Gbp N/A 635.7 GiB
bZonAlb3 81.52 Gbp N/A 266.3 GiB
Arima bZonAlb1 134.39 Gbp N/A 65.8 GiB
bZonAlb3 105.41 Gbp N/A 56.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 5 January 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bZonAlb1 PacBio HiFi (subreads) 1185.51 Gbp N/A 2.0 TiB
PacBio HiFi (.fq) 58.39 Gbp N/A 49.9 GiB
PacBio HiFi (.bam) 178.89 Gbp N/A 635.7 GiB
Arima 134.39 Gbp N/A 65.8 GiB
bZonAlb3 PacBio HiFi (.fq) 79.97 Gbp N/A 39.0 GiB
PacBio HiFi (.bam) 81.52 Gbp N/A 266.3 GiB
Arima 105.41 Gbp N/A 56.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 5 January 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 22 January 2025
bZonAlb1.hap1.cur.20250122.fasta.gz (353.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 67.04 Mbp 1 156.57 Mbp
20 5 42.58 Mbp 2 120.04 Mbp
30 8 35.47 Mbp 3 118.42 Mbp
40 13 21.36 Mbp 5 74.50 Mbp
50 20 17.15 Mbp 7 64.43 Mbp
60 28 13.71 Mbp 9 45.93 Mbp
70 39 9.73 Mbp 12 34.00 Mbp
80 55 6.02 Mbp 18 17.68 Mbp
90 84 3.09 Mbp 27 9.66 Mbp
100 408 11.30 Kbp 179 12.64 Kbp
1.000x 408 1.28 Gbp 179 1.28 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 31 January 2025
bZonAlb1.hap2.cur.20250131.fasta.gz (324.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 120.64 Mbp 1 156.84 Mbp
20 4 43.38 Mbp 2 119.34 Mbp
30 7 27.26 Mbp 3 118.17 Mbp
40 12 20.37 Mbp 5 74.31 Mbp
50 18 18.67 Mbp 6 66.00 Mbp
60 25 15.86 Mbp 8 47.02 Mbp
70 34 11.02 Mbp 12 23.04 Mbp
80 47 6.55 Mbp 18 15.56 Mbp
90 75 2.36 Mbp 28 9.03 Mbp
100 396 543 bp 150 20.25 Kbp
1.000x 396 1.18 Gbp 150 1.18 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
Individual 3 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 6 February 2026
bZonAlb3.HiC.hap1.20260206.fasta.gz (326.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 64.92 Mbp 1 157.49 Mbp
20 4 42.00 Mbp 2 120.64 Mbp
30 8 34.30 Mbp 3 119.75 Mbp
40 12 31.30 Mbp 5 85.92 Mbp
50 16 26.83 Mbp 6 75.41 Mbp
60 22 18.10 Mbp 8 64.74 Mbp
70 30 15.05 Mbp 11 35.89 Mbp
80 40 9.73 Mbp 15 28.95 Mbp
90 59 4.61 Mbp 21 14.26 Mbp
100 245 4.74 Kbp 80 4.74 Kbp
1.000x 245 1.30 Gbp 80 1.30 Gbp
NG based on genome size .
Individual 3 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 6 February 2026
bZonAlb3.HiC.hap2.20260206.fasta.gz (289.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 68.82 Mbp 1 157.61 Mbp
20 4 45.75 Mbp 2 118.90 Mbp
30 7 41.72 Mbp 3 117.67 Mbp
40 10 30.49 Mbp 4 85.41 Mbp
50 15 22.06 Mbp 6 73.10 Mbp
60 21 19.54 Mbp 7 65.73 Mbp
70 27 16.03 Mbp 10 30.43 Mbp
80 36 11.17 Mbp 15 22.29 Mbp
90 50 5.82 Mbp 21 15.20 Mbp
100 174 26.45 Kbp 68 41.60 Kbp
1.000x 174 1.14 Gbp 68 1.14 Gbp
NG based on genome size .
Individual 3 Mitochondrial Assembly
Version assembly_MT_rockefeller from 6 February 2026
bZonAlb3.MT.20260206.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).
assembly_vgp_HiC_2.0/bZonAlb3.yml (view)
species: Zonotrichia albicollis
specimem: bZonAlb3
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Zonotrichia_albicollis/bZonAlb3/assembly_vgp_HiC_2.0/bZonAlb3.HiC.hap1.20260206.fasta.gz
hap2: s3://genomeark/species/Zonotrichia_albicollis/bZonAlb3/assembly_vgp_HiC_2.0/bZonAlb3.HiC.hap2.20260206.fasta.gz
pretext_hap1: s3://genomeark/species/Zonotrichia_albicollis/bZonAlb3/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bZonAlb3_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Zonotrichia_albicollis/bZonAlb3/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bZonAlb3_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Zonotrichia_albicollis/bZonAlb3/assembly_vgp_HiC_2.0/evaluation/merqury/bZonAlb3_png/
pacbio_read_dir: s3://genomeark/species/Zonotrichia_albicollis/bZonAlb3/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Zonotrichia_albicollis/bZonAlb3/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.6)
  - VGP4 HiFi HiC assembly workflow (v0.5)
  - VGP8 HiC scaffolding workflow (v3.3) with mapq=10
  - VGP9 decontamination workflow (v1.2) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of bZonAlb3 resulting in two haplotype assemblies. HiC data were generated using the Arima library prep kit, and require trimming the first 5 bp off from the 5' end of both read files. The restriction enzymes used were the Arima v2 kit, so the cutting sites are GATC, GANTC, CTNAG, TTAA. There are some signs of haplotigs in Merqury copy number plot in hap1. However, running purge-dup workflow (v0.10.4)  didn't seemingly remove these haplotigs. Hence I exported the assembly without purging.
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.