Empidonax oberholseri

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bEmpObe1 49.50 Gbp N/A 22.7 GiB
PacBio HiFi (.bam) bEmpObe1 50.28 Gbp N/A 161.7 GiB
Arima bEmpObe1 139.52 Gbp N/A 72.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 September 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bEmpObe1 PacBio HiFi (.fq) 49.50 Gbp N/A 22.7 GiB
PacBio HiFi (.bam) 50.28 Gbp N/A 161.7 GiB
Arima 139.52 Gbp N/A 72.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 September 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 26 September 2025
bEmpObe1.HiC.hap1.20250926.fasta.gz (292.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 55.67 Mbp 1 117.28 Mbp
20 4 52.71 Mbp 2 116.19 Mbp
30 7 35.76 Mbp 3 97.21 Mbp
40 11 21.26 Mbp 5 74.80 Mbp
50 17 18.52 Mbp 6 74.45 Mbp
60 24 15.21 Mbp 8 55.97 Mbp
70 31 12.54 Mbp 11 31.12 Mbp
80 42 7.75 Mbp 15 21.08 Mbp
90 59 4.86 Mbp 21 15.75 Mbp
100 279 11.80 Kbp 158 11.80 Kbp
1.000x 279 1.09 Gbp 158 1.09 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 26 September 2025
bEmpObe1.HiC.hap2.20250926.fasta.gz (294.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 70.10 Mbp 1 118.60 Mbp
20 4 51.46 Mbp 2 116.07 Mbp
30 6 39.60 Mbp 3 96.96 Mbp
40 10 26.03 Mbp 5 74.83 Mbp
50 14 21.27 Mbp 6 74.81 Mbp
60 20 18.71 Mbp 8 55.64 Mbp
70 28 12.41 Mbp 11 31.19 Mbp
80 38 8.90 Mbp 16 21.27 Mbp
90 55 4.72 Mbp 22 14.94 Mbp
100 309 13.35 Kbp 148 13.35 Kbp
1.000x 309 1.10 Gbp 148 1.10 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 26 September 2025
bEmpObe1.MT.20250926.fasta.gz (5.5 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bEmpObe1.yml (view)
species: Empidonax oberholseri
specimem: bEmpObe1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Empidonax_oberholseri/bEmpObe1/assembly_vgp_HiC_2.0/bEmpObe1.HiC.hap1.20250926.fasta.gz
hap2: s3://genomeark/species/Empidonax_oberholseri/bEmpObe1/assembly_vgp_HiC_2.0/bEmpObe1.HiC.hap2.20250926.fasta.gz
pretext_hap1: s3://genomeark/species/Empidonax_oberholseri/bEmpObe1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bEmpObe1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Empidonax_oberholseri/bEmpObe1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bEmpObe1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Empidonax_oberholseri/bEmpObe1/assembly_vgp_HiC_2.0/evaluation/merqury/bEmpObe1_png/
pacbio_read_dir: s3://genomeark/species/Empidonax_oberholseri/bEmpObe1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Empidonax_oberholseri/bEmpObe1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.12)
  - VGP8 HiC scaffolding workflow (v2.2) with mapq=10
  - VGP9 decontamination workflow unpublished using FCS (0.5.0+galaxy0) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of bEmpObe1 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.