Poecile atricapillus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bPoeAtr1 46.24 Gbp N/A 35.3 GiB
Bionano bPoeAtr1 N/A N/A 1.9 GiB
Arima bPoeAtr1 129.52 Gbp N/A 62.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 August 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bPoeAtr1 PacBio HiFi (.fq) 46.24 Gbp N/A 35.3 GiB
Bionano N/A N/A 1.9 GiB
Arima 129.52 Gbp N/A 62.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 August 2022.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 28 April 2023
bPoeAtr1.hap1.cur.20230428.fasta.gz (349.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 25.00 Mbp 1 181.57 Mbp
20 11 17.02 Mbp 2 154.67 Mbp
30 19 13.13 Mbp 3 146.58 Mbp
40 30 10.32 Mbp 4 116.92 Mbp
50 44 8.46 Mbp 5 107.92 Mbp
60 62 6.17 Mbp 6 76.76 Mbp
70 85 4.26 Mbp 9 34.40 Mbp
80 122 2.69 Mbp 14 20.47 Mbp
90 182 1.54 Mbp 22 11.24 Mbp
100 708 1.00 Kbp 306 1.00 Kbp
1.000x 708 1.25 Gbp 306 1.25 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 30 May 2023
bPoeAtr1.hap2.cur.20230530.fasta.gz (276.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 19.33 Mbp 1 180.92 Mbp
20 10 15.96 Mbp 2 154.83 Mbp
30 17 11.95 Mbp 2 154.83 Mbp
40 26 9.73 Mbp 3 117.24 Mbp
50 38 8.01 Mbp 4 75.87 Mbp
60 53 5.83 Mbp 6 37.92 Mbp
70 72 4.49 Mbp 9 24.31 Mbp
80 99 2.96 Mbp 14 17.70 Mbp
90 141 1.84 Mbp 22 8.54 Mbp
100 397 3.00 Kbp 157 3.00 Kbp
1.000x 397 0.99 Gbp 157 0.99 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/bPoeAtr1_hap1.yml (view)
species: Poecile atricapillus
specimen: bPoeAtr1
projects: 
  - vgp
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Poecile_atricapillus/bPoeAtr1/assembly_vgp_HiC_2.0/bPoeAtr1.HiC.hap1.20220821.fasta.gz
hap2: s3://genomeark/species/Poecile_atricapillus/bPoeAtr1/assembly_vgp_HiC_2.0/bPoeAtr1.HiC.hap2.20220821.fasta.gz
pretext_hap1: s3://genomeark/species/Poecile_atricapillus/bPoeAtr1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bPoeAtr1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Poecile_atricapillus/bPoeAtr1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bPoeAtr1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Poecile_atricapillus/bPoeAtr1/assembly_vgp_HiC_2.0/evaluation/merqury/bPoeAtr1_png/
pacbio_read_dir: s3://genomeark/species/Poecile_atricapillus/bPoeAtr1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Poecile_atricapillus/bPoeAtr1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Poecile_atricapillus/bPoeAtr1/genomic_data/arima/
pipeline:
  - hifiasm (0.16.1-r375)
  - solve (3.7)
  - salsa2
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of bPoeAtr1, resulting in two complete haplotypes. This individual did have bionano data. HiC scaffolding was performed with SALSA2. The HiC prep was Arima kit 2. The kmer spectra indicates a heterogametic specimen, so we are submitting both haplotypes as tickets, in case the sex chromosomes need to be fished out between the haplotypes. This is the curation ticket for hap1.
assembly_vgp_HiC_2.0/bPoeAtr1_hap2.yml (view)
species: Poecile atricapillus
specimen: bPoeAtr1
projects: 
  - vgp
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Poecile_atricapillus/bPoeAtr1/assembly_vgp_HiC_2.0/bPoeAtr1.HiC.hap1.20220821.fasta.gz
hap2: s3://genomeark/species/Poecile_atricapillus/bPoeAtr1/assembly_vgp_HiC_2.0/bPoeAtr1.HiC.hap2.20220821.fasta.gz
pretext_hap1: s3://genomeark/species/Poecile_atricapillus/bPoeAtr1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bPoeAtr1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Poecile_atricapillus/bPoeAtr1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bPoeAtr1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Poecile_atricapillus/bPoeAtr1/assembly_vgp_HiC_2.0/evaluation/merqury/bPoeAtr1_png/
pacbio_read_dir: s3://genomeark/species/Poecile_atricapillus/bPoeAtr1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Poecile_atricapillus/bPoeAtr1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Poecile_atricapillus/bPoeAtr1/genomic_data/arima/
pipeline:
  - hifiasm (0.16.1-r375)
  - solve (3.7)
  - salsa2
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of bPoeAtr1, resulting in two complete haplotypes. This individual did have bionano data. HiC scaffolding was performed with SALSA2. The HiC prep was Arima kit 2. The kmer spectra indicates a heterogametic specimen, so we are submitting both haplotypes as tickets, in case the sex chromosomes need to be fished out between the haplotypes. This is the curation ticket for hap2.
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.