Myioborus ornatus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 24 June 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 24 June 2025.
Assemblies
Individual 2 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 10 July 2025
bMyiOra2.HiC.hap1.20250710.fasta.gz (321.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 108.82 Mbp 1 158.92 Mbp
20 3 85.85 Mbp 2 130.61 Mbp
30 4 78.30 Mbp 3 120.65 Mbp
40 6 72.53 Mbp 5 80.84 Mbp
50 9 32.39 Mbp 7 72.53 Mbp
60 14 27.13 Mbp 9 40.31 Mbp
70 19 22.92 Mbp 13 26.21 Mbp
80 27 13.49 Mbp 19 18.33 Mbp
90 40 6.27 Mbp 29 9.60 Mbp
100 203 13.47 Kbp 132 13.47 Kbp
1.000x 203 1.32 Gbp 132 1.32 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 10 July 2025
bMyiOra2.HiC.hap2.20250710.fasta.gz (289.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 127.56 Mbp 1 158.62 Mbp
20 3 77.40 Mbp 2 128.21 Mbp
30 4 66.55 Mbp 3 117.49 Mbp
40 6 59.61 Mbp 4 79.53 Mbp
50 9 39.83 Mbp 6 74.44 Mbp
60 12 28.19 Mbp 8 39.83 Mbp
70 17 22.52 Mbp 12 26.56 Mbp
80 24 13.15 Mbp 18 15.64 Mbp
90 37 6.28 Mbp 27 9.93 Mbp
100 175 20.05 Kbp 98 24.63 Kbp
1.000x 175 1.19 Gbp 98 1.19 Gbp
NG based on genome size .
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 10 July 2025
bMyiOra2.MT.20250710.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bMyiOra2.yml (view)
species: Myioborus ornatus
specimem: bMyiOra2
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Myioborus_ornatus/bMyiOra2/assembly_vgp_HiC_2.0/bMyiOra2.HiC.hap1.20250710.fasta.gz
hap2: s3://genomeark/species/Myioborus_ornatus/bMyiOra2/assembly_vgp_HiC_2.0/bMyiOra2.HiC.hap2.20250710.fasta.gz
pretext_hap1: s3://genomeark/species/Myioborus_ornatus/bMyiOra2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bMyiOra2_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Myioborus_ornatus/bMyiOra2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bMyiOra2_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Myioborus_ornatus/bMyiOra2/assembly_vgp_HiC_2.0/evaluation/merqury/bMyiOra2_png/
pacbio_read_dir: s3://genomeark/species/Myioborus_ornatus/bMyiOra2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Myioborus_ornatus/bMyiOra2/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.1)
  - VGP1 genomic profiling workflow (v0.3)
  - VGP4 HiFi HiC assembly workflow (v0.3.8)
  - VGP8 HiC scaffolding workflow (v2.0)
  - VGP9 decontamination workflow (v0.7) with database PlusPF 2022
  - Pre-curation worklfow (v1.0beta6)
notes: This was a Hifiasm-HiC assembly of bMyiOra2 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.