Spinus tristis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bSpiTri1 1216.67 Gbp N/A 2.1 TiB
PacBio HiFi (.fq) bSpiTri1 51.91 Gbp N/A 39.1 GiB
Arima bSpiTri1 70.67 Gbp N/A 36.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 26 March 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bSpiTri1 PacBio HiFi (subreads) 1216.67 Gbp N/A 2.1 TiB
PacBio HiFi (.fq) 51.91 Gbp N/A 39.1 GiB
Arima 70.67 Gbp N/A 36.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 26 March 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 26 February 2026
bSpiTri1.hap1.cur.20260226.fasta.gz (357.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 33.32 Mbp 1 156.12 Mbp
20 8 22.23 Mbp 2 124.09 Mbp
30 15 17.53 Mbp 4 101.75 Mbp
40 24 13.73 Mbp 5 83.49 Mbp
50 35 10.38 Mbp 7 67.58 Mbp
60 49 8.37 Mbp 9 47.91 Mbp
70 70 4.53 Mbp 12 32.14 Mbp
80 110 2.67 Mbp 17 21.37 Mbp
90 183 1.24 Mbp 25 9.12 Mbp
100 742 5.34 Kbp 286 5.34 Kbp
1.000x 742 1.35 Gbp 286 1.35 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 26 February 2026
bSpiTri1.hap2.cur.20260226.fasta.gz (326.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 27.31 Mbp 1 155.32 Mbp
20 9 19.96 Mbp 2 123.48 Mbp
30 16 15.95 Mbp 3 121.09 Mbp
40 24 14.24 Mbp 5 73.55 Mbp
50 34 11.31 Mbp 6 68.83 Mbp
60 47 7.63 Mbp 9 40.58 Mbp
70 66 5.27 Mbp 13 28.66 Mbp
80 96 2.98 Mbp 18 16.90 Mbp
90 156 1.39 Mbp 31 5.96 Mbp
100 614 1.46 Kbp 278 15.00 Kbp
1.000x 614 1.22 Gbp 278 1.22 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 6 February 2026
bSpiTri1.MT.20260206.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bSpiTri1.yml (view)
species: Spinus tristis
specimen: bSpiTri1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Spinus_tristis/bSpiTri1/assembly_vgp_HiC_2.0/bSpiTri1.HiC.hap1.20240426.fasta.gz
hap2: s3://genomeark/species/Spinus_tristis/bSpiTri1/assembly_vgp_HiC_2.0/bSpiTri1.HiC.hap2.20240426.fasta.gz
pretext_hap1: s3://genomeark/species/Spinus_tristis/bSpiTri1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bSpiTri1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Spinus_tristis/bSpiTri1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bSpiTri1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Spinus_tristis/bSpiTri1/assembly_vgp_HiC_2.0/evaluation/merqury/bSpiTri1_png/
pacbio_read_dir: s3://genomeark/species/Spinus_tristis/bSpiTri1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Spinus_tristis/bSpiTri1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Spinus_tristis/bSpiTri1/genomic_data/arima/
mito: s3://genomeark/species/Spinus_tristis/bSpiTri1/assembly_MT_rockefeller/bSpiTri1.MT.20240426.fasta.gz
pipeline: 
  - hifiasm (0.19.8+galaxy1)
  - solve (3.7)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of bSpiTri1, resulting in two complete haplotypes. HiC scaffolding was performed with 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.