Atlapetes fuscoolivaceus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bAtlFus1 59.71 Gbp N/A 42.6 GiB
bAtlFus2 70.50 Gbp N/A 33.6 GiB
PacBio HiFi (.bam) bAtlFus2 71.71 Gbp N/A 220.3 GiB
Arima bAtlFus2 78.60 Gbp N/A 42.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 7 July 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bAtlFus1 PacBio HiFi (.fq) 59.71 Gbp N/A 42.6 GiB
bAtlFus2 PacBio HiFi (.fq) 70.50 Gbp N/A 33.6 GiB
PacBio HiFi (.bam) 71.71 Gbp N/A 220.3 GiB
Arima 78.60 Gbp N/A 42.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 7 July 2025.
Assemblies
Individual 2 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 23 September 2025
bAtlFus2.HiC.hap1.20250923.fasta.gz (309.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 74.55 Mbp 1 160.59 Mbp
20 5 42.62 Mbp 2 124.38 Mbp
30 8 33.76 Mbp 3 108.26 Mbp
40 13 24.59 Mbp 5 80.79 Mbp
50 18 19.24 Mbp 7 67.77 Mbp
60 25 16.60 Mbp 9 40.02 Mbp
70 35 10.43 Mbp 14 23.32 Mbp
80 52 4.78 Mbp 21 13.43 Mbp
90 103 1.27 Mbp 34 5.12 Mbp
100 604 19.25 Kbp 358 19.25 Kbp
1.000x 604 1.29 Gbp 358 1.29 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 23 September 2025
bAtlFus2.HiC.hap2.20250923.fasta.gz (301.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 55.41 Mbp 1 161.63 Mbp
20 6 30.39 Mbp 2 128.33 Mbp
30 10 27.33 Mbp 3 115.84 Mbp
40 15 22.88 Mbp 4 84.65 Mbp
50 21 17.90 Mbp 6 80.96 Mbp
60 28 13.13 Mbp 8 41.66 Mbp
70 39 8.79 Mbp 11 25.90 Mbp
80 61 3.89 Mbp 16 19.82 Mbp
90 109 1.57 Mbp 25 7.64 Mbp
100 432 26.00 Kbp 217 26.00 Kbp
1.000x 432 1.20 Gbp 217 1.20 Gbp
NG based on genome size .
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 23 September 2025
bAtlFus2.MT.20250923.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bAtlFus2.yml (view)
species: Atlapetes fuscoolivaceus
specimem: bAtlFus2
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Atlapetes_fuscoolivaceus/bAtlFus2/assembly_vgp_HiC_2.0/bAtlFus2.HiC.hap1.20250923.fasta.gz
hap2: s3://genomeark/species/Atlapetes_fuscoolivaceus/bAtlFus2/assembly_vgp_HiC_2.0/bAtlFus2.HiC.hap2.20250923.fasta.gz
pretext_hap1: s3://genomeark/species/Atlapetes_fuscoolivaceus/bAtlFus2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bAtlFus2_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Atlapetes_fuscoolivaceus/bAtlFus2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bAtlFus2_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Atlapetes_fuscoolivaceus/bAtlFus2/assembly_vgp_HiC_2.0/evaluation/merqury/bAtlFus2_png/
pacbio_read_dir: s3://genomeark/species/Atlapetes_fuscoolivaceus/bAtlFus2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Atlapetes_fuscoolivaceus/bAtlFus2/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 (v0.5.5+galaxy0) 
  - Pre-curation worklfow (v1.obeta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of bAtlFus2 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.