Sitta carolinensis

white-breasted nuthatches

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  name: Sitta carolinensis
  individuals:
  - short_name: bSitCar2
  short_name: bSitCar
  taxon_id: 50250
  common_name: white-breasted nuthatches
  genome_size: 1193000000
  genome_size_method: GoAT
  order:
    name: Passeriformes
  family:
    name: Sittidae
  project: [ vgp ]
CC BY 2.0 Judy Gallagher (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bSitCar1 66.72 Gbp 55.92x 35.5 GiB
PacBio HiFi (.bam) bSitCar1 66.70 Gbp 55.91x 271.0 GiB
Arima bSitCar1 79.88 Gbp 66.95x 40.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.19 Gbp.
Last upload on 5 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bSitCar1 PacBio HiFi (.fq) 66.72 Gbp 55.92x 35.5 GiB
PacBio HiFi (.bam) 66.70 Gbp 55.91x 271.0 GiB
Arima 79.88 Gbp 66.95x 40.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.19 Gbp.
Last upload on 5 June 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 13 June 2024
bSitCar1.HiC.hap1.20240613.fasta.gz (312.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 51.31 Mbp 1 163.30 Mbp
20 5 44.75 Mbp 2 117.91 Mbp
30 9 29.76 Mbp 3 77.43 Mbp
40 14 16.44 Mbp 5 71.10 Mbp
50 22 14.44 Mbp 7 45.48 Mbp
60 32 10.69 Mbp 11 26.93 Mbp
70 45 7.76 Mbp 16 20.13 Mbp
80 65 4.28 Mbp 23 13.38 Mbp
90 125 0.85 Mbp 39 2.81 Mbp
100 0 0
0.941x 453 1.12 Gbp 248 1.13 Gbp
NG based on genome size 1.19 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 13 June 2024
bSitCar1.HiC.hap2.20240613.fasta.gz (309.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 32.13 Mbp 2 117.03 Mbp
20 8 26.24 Mbp 3 73.66 Mbp
30 13 18.21 Mbp 4 71.11 Mbp
40 21 13.89 Mbp 6 44.54 Mbp
50 30 11.67 Mbp 9 35.95 Mbp
60 42 8.88 Mbp 13 23.43 Mbp
70 61 4.84 Mbp 19 17.83 Mbp
80 96 2.51 Mbp 28 9.62 Mbp
90 190 0.66 Mbp 61 1.36 Mbp
100 0 0
0.955x 571 1.14 Gbp 339 1.15 Gbp
NG based on genome size 1.19 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 13 June 2024
bSitCar1.MT.20240613.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bSitCar1.yml (view)
species: Sitta carolinensis
specimen: bSitCar1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Sitta_carolinensis/bSitCar1/assembly_vgp_HiC_2.0/bSitCar1.HiC.hap1.30240613.fasta.gz
hap2: s3://genomeark/species/Sitta_carolinensis/bSitCar1/assembly_vgp_HiC_2.0/bSitCar1.HiC.hap2.20240361.fasta.gz
pretext_hap1: s3://genomeark/species/Sitta_carolinensis/bSitCar1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bSitCar1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Sitta_carolinensis/bSitCar1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bSitCar1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Sitta_carolinensis/bSitCar1/assembly_vgp_HiC_2.0/evaluation/merqury/hap1_purged/bSitCar1_png/
pacbio_read_dir: s3://genomeark/species/Sitta_carolinensis/bSitCar1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Sitta_carolinensis/bSitCar1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Sitta_carolinensis/bSitCar1/genomic_data/arima/
mito: s3://genomeark/species/Sitta_carolinensis/bSitCar1/assembly_MT_rockefeller/bSitCar1.MT.20240613.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 bSitCar1, resulting in two complete haplotypes. Each haplotype underwent purging (while keeping repeats), and then 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). The VGL ID for this specimen is VGL-bSitCar2.
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.