Sayornis phoebe

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Resource Primary Assembly Alternate Assembly
GenBank bSayPho2: GCA_051295625.1 bSayPho2: GCA_051295565.1
ENA bSayPho2: GCA_051295625.1 bSayPho2: GCA_051295565.1
UCSC Genome Browser bSayPho2: GCA_051295625.1 bSayPho2: GCA_051295565.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bSayPho3 67.64 Gbp N/A 31.5 GiB
PacBio HiFi (.bam) bSayPho3 69.41 Gbp N/A 224.4 GiB
Arima bSayPho3 108.31 Gbp N/A 57.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 18 April 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bSayPho3 PacBio HiFi (.fq) 67.64 Gbp N/A 31.5 GiB
PacBio HiFi (.bam) 69.41 Gbp N/A 224.4 GiB
Arima 108.31 Gbp N/A 57.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 18 April 2025.
Assemblies
Individual 3 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 19 May 2025
bSayPho3.HiC.hap1.20250519.fasta.gz (284.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 55.46 Mbp 1 157.49 Mbp
20 5 35.40 Mbp 2 146.64 Mbp
30 8 30.39 Mbp 3 125.72 Mbp
40 12 26.94 Mbp 4 119.02 Mbp
50 17 20.89 Mbp 5 77.27 Mbp
60 23 16.37 Mbp 6 74.88 Mbp
70 31 11.08 Mbp 7 74.56 Mbp
80 43 7.65 Mbp 11 21.64 Mbp
90 63 3.70 Mbp 17 15.93 Mbp
100 448 13.64 Kbp 258 13.64 Kbp
1.000x 448 1.10 Gbp 258 1.10 Gbp
NG based on genome size .
Individual 3 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 19 May 2025
bSayPho3.HiC.hap2.20250519.fasta.gz (291.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 43.61 Mbp 1 183.31 Mbp
20 5 35.65 Mbp 2 115.52 Mbp
30 9 25.84 Mbp 3 99.43 Mbp
40 14 21.84 Mbp 4 91.28 Mbp
50 19 17.36 Mbp 5 74.93 Mbp
60 27 12.04 Mbp 7 56.19 Mbp
70 36 9.59 Mbp 9 41.70 Mbp
80 48 8.16 Mbp 13 23.03 Mbp
90 66 4.22 Mbp 18 16.28 Mbp
100 261 17.91 Kbp 129 17.91 Kbp
1.000x 261 1.10 Gbp 129 1.10 Gbp
NG based on genome size .
Individual 3 Mitochondrial Assembly
Version assembly_MT_rockefeller from 12 May 2025
bSayPho3.MT.20250512.fasta.gz (5.5 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bSayPho3.yml (view)
species: Sayornis phoebe
specimem: bSayPho3
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Sayornis_phoebe/bSayPho3/assembly_vgp_HiC_2.0/bSayPho3.HiC.hap1.20250519.fasta.gz
hap2: s3://genomeark/species/Sayornis_phoebe/bSayPho3/assembly_vgp_HiC_2.0/bSayPho3.HiC.hap2.20250519.fasta.gz
pretext_hap1: s3://genomeark/species/Sayornis_phoebe/bSayPho3/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bSayPho3_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Sayornis_phoebe/bSayPho3/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bSayPho3_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Sayornis_phoebe/bSayPho3/assembly_vgp_HiC_2.0/evaluation/merqury/bSayPho3_png/
pacbio_read_dir: s3://genomeark/species/Sayornis_phoebe/bSayPho3/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Sayornis_phoebe/bSayPho3/genomic_data/arima/
pipeline:
  - hifiasm (0.24.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
notes: This was a Hifiasm-HiC assembly of bSayPho3 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.
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.