Lathamus discolor

Swift parrot

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  name: Lathamus discolor
  individuals:
  - short_name: bLatDis1
  short_name: bLatDis
  taxon_id: 678569
  common_name: Swift parrot
  genome_size: 1385000000
  genome_size_method: GoAT
  order:
    name: Psittaciformes
  family:
    name: Psittacidae
  project: [ vgp ]
CC BY-NC-SA 2.0 David Jenkins (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bLatDis1 43.50 Gbp 31.40x 34.6 GiB
Arima bLatDis1 142.75 Gbp 103.07x 71.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.39 Gbp.
Last upload on 11 April 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bLatDis1 PacBio HiFi (.fq) 43.50 Gbp 31.40x 34.6 GiB
Arima 142.75 Gbp 103.07x 71.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.39 Gbp.
Last upload on 11 April 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 10 July 2023
bLatDis1.hap1.cur.20230710.fasta.gz (315.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 43.45 Mbp 1 166.04 Mbp
20 6 38.47 Mbp 2 160.32 Mbp
30 10 30.90 Mbp 3 152.78 Mbp
40 15 23.64 Mbp 4 128.18 Mbp
50 22 16.32 Mbp 5 126.11 Mbp
60 32 11.93 Mbp 6 112.48 Mbp
70 45 8.73 Mbp 8 41.83 Mbp
80 68 2.97 Mbp 15 13.13 Mbp
90 0 0
100 0 0
0.894x 553 1.24 Gbp 367 1.24 Gbp
NG based on genome size 1.39 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 10 July 2023
bLatDis1.hap2.cur.20230710.fasta.gz (281.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 56.53 Mbp 1 167.12 Mbp
20 5 44.03 Mbp 2 161.57 Mbp
30 9 30.36 Mbp 3 154.80 Mbp
40 14 25.14 Mbp 4 129.02 Mbp
50 20 19.23 Mbp 5 128.19 Mbp
60 30 11.27 Mbp 6 92.27 Mbp
70 48 5.17 Mbp 13 13.09 Mbp
80 330 95.61 Kbp 194 114.33 Kbp
90 0 0
100 0 0
0.809x 535 1.12 Gbp 413 1.12 Gbp
NG based on genome size 1.39 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 10 July 2023
bLatDis1.MT.20230710.fasta.gz (5.7 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bLatDis1.yml (view)
species: Lathamus discolor
specimen: bLatDis1
projects: 
  - vgp
hap1: s3://genomeark/species/Lathamus_discolor/bLatDis1/assembly_vgp_HiC_2.0/bLatDis1.HiC.hap1.20230710.fasta.gz
hap2: s3://genomeark/species/Lathamus_discolor/bLatDis1/assembly_vgp_HiC_2.0/bLatDis1.HiC.hap2.20230710.fasta.gz
pretext_hap1: s3://genomeark/species/Lathamus_discolor/bLatDis1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bLatDis1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Lathamus_discolor/bLatDis1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bLatDis1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Lathamus_discolor/bLatDis1/assembly_vgp_HiC_2.0/evaluation/merqury/bLatDis1_png/
mito: s3://genomeark/species/Lathamus_discolor/bLatDis1/assembly_MT_rockefeller/bLatDis1.MT.20230710.fasta.gz
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - solve (3.7)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of bLatDis1, resulting in two complete haplotypes. This individual did bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2.
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.