Spizella passerina

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bSpiPas1 1403.95 Gbp N/A 2.4 TiB
PacBio HiFi (.fq) bSpiPas1 65.63 Gbp N/A 47.0 GiB
Arima bSpiPas1 82.63 Gbp N/A 42.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 27 March 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bSpiPas1 PacBio HiFi (subreads) 1403.95 Gbp N/A 2.4 TiB
PacBio HiFi (.fq) 65.63 Gbp N/A 47.0 GiB
Arima 82.63 Gbp N/A 42.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 27 March 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 16 July 2024
bSpiPas1.HiC.hap1.20240716.fasta.gz (344.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 16.23 Mbp 2 115.58 Mbp
20 14 12.99 Mbp 3 98.57 Mbp
30 25 10.33 Mbp 4 76.15 Mbp
40 39 7.44 Mbp 6 66.59 Mbp
50 60 5.16 Mbp 8 40.02 Mbp
60 87 4.04 Mbp 12 28.62 Mbp
70 124 2.71 Mbp 17 18.85 Mbp
80 182 1.64 Mbp 25 12.46 Mbp
90 282 0.88 Mbp 43 4.09 Mbp
100 780 11.83 Kbp 308 11.83 Kbp
1.000x 780 1.25 Gbp 308 1.25 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 16 July 2024
bSpiPas1.HiC.hap2.20240716.fasta.gz (354.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 7 14.29 Mbp 2 118.39 Mbp
20 17 11.44 Mbp 3 99.98 Mbp
30 29 9.39 Mbp 4 97.60 Mbp
40 44 7.28 Mbp 6 74.58 Mbp
50 65 5.39 Mbp 7 65.14 Mbp
60 93 3.87 Mbp 10 40.13 Mbp
70 134 2.54 Mbp 14 27.16 Mbp
80 194 1.72 Mbp 20 15.81 Mbp
90 291 1.03 Mbp 35 5.56 Mbp
100 706 15.08 Kbp 201 15.08 Kbp
1.000x 706 1.27 Gbp 201 1.29 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 18 July 2024
bSpiPas1.MT.20240718.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bSpiPas1.yml (view)
species: Spizella passerina
specimen: bSpiPas1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Spizella_passerina/bSpiPas1/assembly_vgp_HiC_2.0/bSpiPas1.HiC.hap1.20240716.fasta.gz
hap2: s3://genomeark/species/Spizella_passerina/bSpiPas1/assembly_vgp_HiC_2.0/bSpiPas1.HiC.hap2.20240716.fasta.gz
pretext_hap1: s3://genomeark/species/Spizella_passerina/bSpiPas1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bSpiPas1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Spizella_passerina/bSpiPas1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bSpiPas1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Spizella_passerina/bSpiPas1/assembly_vgp_HiC_2.0/evaluation/merqury/hap1_purged/bSpiPas1_png/
pacbio_read_dir: s3://genomeark/species/Spizella_passerina/bSpiPas1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Spizella_passerina/bSpiPas1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Spizella_passerina/bSpiPas1/genomic_data/arima/
mito: s3://genomeark/species/Spizella_passerina/bSpiPas1/assembly_MT_rockefeller/bSpiPas1.MT.20240718.fasta.gz
pipeline: 
  - hifiasm (0.19.8+galaxy1)
  - solve (3.7.0+galaxy3)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of bSpiPas1, resulting in two complete haplotypes. The scaffolding consisted of Bionano Solve and YaHS.  The HiC prep kit used was Swift-IDT. The assembly was performed on usegalaxy MAIN server (vgp.usegalaxy.org). 
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.