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_vgp_HiC_2.0 from 26 April 2024
bSpiTri1.HiC.hap1.20240426.fasta.gz (321.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 27.99 Mbp 1 153.46 Mbp
20 8 22.23 Mbp 2 119.57 Mbp
30 14 18.90 Mbp 3 118.45 Mbp
40 21 15.65 Mbp 5 73.19 Mbp
50 30 12.16 Mbp 6 67.58 Mbp
60 42 9.12 Mbp 9 33.11 Mbp
70 58 5.05 Mbp 13 21.62 Mbp
80 90 2.74 Mbp 21 11.76 Mbp
90 148 1.38 Mbp 37 3.97 Mbp
100 630 5.34 Kbp 332 5.34 Kbp
1.000x 630 1.18 Gbp 332 1.18 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 26 April 2024
bSpiTri1.HiC.hap2.20240426.fasta.gz (374.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 28.18 Mbp 1 156.12 Mbp
20 10 19.26 Mbp 3 118.64 Mbp
30 18 15.44 Mbp 4 79.66 Mbp
40 28 12.99 Mbp 6 68.83 Mbp
50 40 10.12 Mbp 8 36.32 Mbp
60 57 7.07 Mbp 13 28.18 Mbp
70 81 4.44 Mbp 19 16.90 Mbp
80 122 2.55 Mbp 31 8.37 Mbp
90 202 1.25 Mbp 59 2.65 Mbp
100 733 15.00 Kbp 364 15.00 Kbp
1.000x 733 1.41 Gbp 364 1.41 Gbp
NG based on genome size .
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.