Spizella passerina

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


Resource Primary Assembly Alternate Assembly
GenBank bSpiPas2: GCA_051176105.1 bSpiPas2: GCA_051176095.1
ENA bSpiPas2: GCA_051176105.1 bSpiPas2: GCA_051176095.1
UCSC Genome Browser bSpiPas2: GCA_051176105.1 bSpiPas2: GCA_051176095.1

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
PacBio HiFi (.bam) bSpiPas1 198.95 Gbp N/A 681.5 GiB
Arima bSpiPas1 82.63 Gbp N/A 42.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 February 2026.
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
PacBio HiFi (.bam) 198.95 Gbp N/A 681.5 GiB
Arima 82.63 Gbp N/A 42.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 February 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 4 February 2026
bSpiPas1.hap1.cur.20260204.fasta.gz (373.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 15.55 Mbp 2 116.80 Mbp
20 16 12.61 Mbp 3 100.10 Mbp
30 28 10.32 Mbp 4 98.57 Mbp
40 44 7.35 Mbp 6 75.23 Mbp
50 66 5.18 Mbp 8 59.99 Mbp
60 96 3.99 Mbp 11 45.18 Mbp
70 137 2.67 Mbp 14 29.13 Mbp
80 199 1.67 Mbp 19 16.59 Mbp
90 305 0.91 Mbp 31 8.98 Mbp
100 842 4.26 Kbp 260 11.83 Kbp
1.000x 842 1.35 Gbp 260 1.35 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 4 February 2026
bSpiPas1.hap2.cur.20260204.fasta.gz (295.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 15.65 Mbp 1 123.91 Mbp
20 15 12.10 Mbp 2 118.53 Mbp
30 26 10.02 Mbp 4 76.05 Mbp
40 40 7.28 Mbp 5 74.58 Mbp
50 58 5.06 Mbp 7 60.89 Mbp
60 85 3.93 Mbp 10 41.70 Mbp
70 122 2.54 Mbp 13 29.48 Mbp
80 178 1.66 Mbp 18 15.81 Mbp
90 269 0.92 Mbp 29 8.66 Mbp
100 670 7.79 Kbp 159 15.08 Kbp
1.000x 670 1.17 Gbp 159 1.19 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.