Colius striatus

speckled mousebird

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank bColStr4: GCA_028858625.1 bColStr4: GCA_028858725.1
ENA bColStr4: GCA_028858625.1 bColStr4: GCA_028858725.1
UCSC Genome Browser bColStr4: GCA_028858625.1 bColStr4: GCA_028858725.1

metadata.yaml (view) (edit on github)
species:
  name: Colius striatus
  individuals:
  - short_name: bColStr4
  short_name: bColStr
  taxon_id: 57412
  common_name: speckled mousebird
  genome_size: 1438000000
  genome_size_method: GoAT
  order:
    name: Coliiformes
  family:
    name: Coliidae
  project: [ vgp ]
CC BY-SA 2.0 Dominic Sherony (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bColStr4 41.57 Gbp 28.91x 34.6 GiB
Bionano bColStr4 N/A 894.68x 2.6 GiB
Arima bColStr4 82.71 Gbp 57.52x 42.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.44 Gbp.
Last upload on 26 April 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bColStr4 PacBio HiFi (.fq) 41.57 Gbp 28.91x 34.6 GiB
Bionano N/A 894.68x 2.6 GiB
Arima 82.71 Gbp 57.52x 42.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.44 Gbp.
Last upload on 26 April 2022.
Assemblies
Individual 4 Haplotype 1 Assembly
Version assembly_curated from 16 February 2023
bColStr4.hap1.cur.20230216.fasta.gz (320.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 67.04 Mbp 0 206.59 Mbp
20 4 39.24 Mbp 1 122.59 Mbp
30 8 30.49 Mbp 3 97.55 Mbp
40 14 22.07 Mbp 4 59.13 Mbp
50 21 15.95 Mbp 7 42.32 Mbp
60 32 9.67 Mbp 12 28.60 Mbp
70 61 2.60 Mbp 19 12.93 Mbp
80 0 0
90 0 0
100 0 0
0.777x 332 1.12 Gbp 189 1.12 Gbp
NG based on genome size 1.44 Gbp.
Individual 4 Haplotype 2 Assembly
Version assembly_curated from 16 February 2023
bColStr4.hap2.cur.20230216.fasta.gz (346.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 49.04 Mbp 0 209.83 Mbp
20 6 32.24 Mbp 1 122.58 Mbp
30 11 26.13 Mbp 2 101.19 Mbp
40 17 21.72 Mbp 4 89.02 Mbp
50 25 14.89 Mbp 6 47.68 Mbp
60 37 10.65 Mbp 10 34.39 Mbp
70 55 5.89 Mbp 15 23.51 Mbp
80 101 1.84 Mbp 28 5.88 Mbp
90 0 0
100 0 0
0.860x 394 1.24 Gbp 243 1.24 Gbp
NG based on genome size 1.44 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/bColStr4.yaml (view)
species: Colius striatus
specimen: bColStr4
projects:
  - vgp
hap1: s3://genomeark/species/Colius_striatus/bColStr4/assembly_vgp_HiC_2.0/bColStr4.HiC.hap1.20220601.fasta.gz
hap2: s3://genomeark/species/Colius_striatus/bColStr4/assembly_vgp_HiC_2.0/bColStr4.HiC.hap2.20220601.fasta.gz
hap1_hic_bam: s3://genomeark/species/Colius_striatus/bColStr4/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bColStr4_hap1__s2.bam
hap2_hic_bam: s3://genomeark/species/Colius_striatus/bColStr4/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bColStr4_hap2__s2.bam
hap1_pretext: s3://genomeark/species/Colius_striatus/bColStr4/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bColStr4_hap1__s2_heatmap.pretext
hap2_pretext: s3://genomeark/species/Colius_striatus/bColStr4/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bColStr4_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Colius_striatus/bColStr4/assembly_vgp_HiC_2.0/evaluation/merqury/bColStr4_png/
pipeline:
  - hifiasm (0.16.1+galaxy2)
  - solve (3.7)
  - salsa (2.3+galaxy2)
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.