Passer domesticus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bPasDom1 454.14 Gbp N/A 790.1 GiB
PacBio HiFi (.fq) bPasDom1 61.54 Gbp N/A 54.0 GiB
Dovetail Genomics bPasDom1 200.17 Gbp N/A 99.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 May 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bPasDom1 PacBio HiFi (subreads) 454.14 Gbp N/A 790.1 GiB
PacBio HiFi (.fq) 61.54 Gbp N/A 54.0 GiB
Dovetail Genomics 200.17 Gbp N/A 99.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 May 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 5 August 2023
bPasDom1.hap1.cur.20230805.fasta.gz (344.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 55.49 Mbp 1 161.09 Mbp
20 5 49.71 Mbp 2 127.38 Mbp
30 8 35.51 Mbp 3 123.61 Mbp
40 12 29.72 Mbp 5 84.38 Mbp
50 17 20.59 Mbp 6 83.07 Mbp
60 24 15.66 Mbp 8 62.69 Mbp
70 33 12.53 Mbp 11 46.52 Mbp
80 47 6.69 Mbp 14 23.72 Mbp
90 77 2.71 Mbp 22 12.53 Mbp
100 535 2.00 Kbp 333 2.00 Kbp
1.000x 535 1.31 Gbp 333 1.31 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 8 August 2023
bPasDom1.hap2.cur.20230808.fasta.gz (330.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 48.11 Mbp 1 162.12 Mbp
20 6 40.56 Mbp 2 129.48 Mbp
30 9 29.69 Mbp 3 121.33 Mbp
40 14 23.46 Mbp 5 77.87 Mbp
50 21 15.03 Mbp 6 74.92 Mbp
60 30 12.62 Mbp 8 61.89 Mbp
70 42 8.30 Mbp 10 44.61 Mbp
80 62 5.12 Mbp 16 15.63 Mbp
90 101 1.83 Mbp 28 6.40 Mbp
100 663 1.00 Kbp 481 1.00 Kbp
1.000x 663 1.26 Gbp 481 1.26 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/bPasDom1.yaml (view)
species: Passer domesticus
specimen: bPasDom1
projects:
  - erga       
  - vgp
hap1: s3://genomeark/species/Passer_domesticus/bPasDom1/assembly_vgp_HiC_2.0/bPasDom1.HiC.hap1.20230510.fasta.gz
hap2: s3://genomeark/species/Passer_domesticus/bPasDom1/assembly_vgp_HiC_2.0/bPasDom1.HiC.hap2.20230510.fasta.gz
primary: 
pretext_hap1: s3://genomeark/species/Passer_domesticus/bPasDom1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bPasDom1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Passer_domesticus/bPasDom1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bPasDom1_hap2_s2_heatmap.pretext
pretext_primary:
kmer_spectra_img: s3://genomeark/species/Passer_domesticus/bPasDom1/assembly_vgp_HiC_2.0/evaluation/merqury/bPasDom1_png/
pacbio_read_dir: s3://genomeark/species/Passer_domesticus/bPasDom1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Passer_domesticus/bPasDom1/genomic_data/dovetail/
hic_kit: Dovetail OmniC
pipeline:
  - hifiasm (0.19.3-r575)
  - yahs (1.2a.1)
notes: This was a hifiasm-HiC assembly of bPasDom1, resulting in two complete haplotypes. This assembly was done by Gabriel David, Uppsala university, Sweden. contact: gbdnorden@gmail.com
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.