Copsychus sechellarum

Seychelles magpie-robin

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  name: Copsychus sechellarum
  individuals:
  - short_name: bCopSec1
  short_name: bCopSec
  taxon_id: 797021
  common_name: Seychelles magpie-robin
  genome_size: 1261000000
  genome_size_method: GoAT
  order:
    name: Passeriformes
  family:
    name: Muscicapidae
  project: [ vgp ]
CC BY-SA 2.0 Adrian Scottow (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bCopSec1 49.71 Gbp 39.42x 37.5 GiB
Arima bCopSec1 75.99 Gbp 60.26x 39.0 GiB
Illumina bCopSec2 59.35 Gbp 47.07x 27.3 GiB
bCopSec3 122.36 Gbp 97.04x 57.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.26 Gbp.
Last upload on 21 April 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bCopSec1 PacBio HiFi (.fq) 49.71 Gbp 39.42x 37.5 GiB
Arima 75.99 Gbp 60.26x 39.0 GiB
bCopSec2 Illumina 59.35 Gbp 47.07x 27.3 GiB
bCopSec3 Illumina 122.36 Gbp 97.04x 57.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.26 Gbp.
Last upload on 21 April 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 4 September 2024
bCopSec1.HiC.hap1.20240904.fasta.gz (344.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 44.56 Mbp 1 156.13 Mbp
20 7 26.28 Mbp 2 121.37 Mbp
30 12 21.51 Mbp 3 114.12 Mbp
40 18 18.41 Mbp 5 76.74 Mbp
50 25 16.08 Mbp 7 65.05 Mbp
60 35 10.29 Mbp 9 41.23 Mbp
70 51 6.61 Mbp 14 23.08 Mbp
80 74 4.29 Mbp 20 17.12 Mbp
90 112 2.47 Mbp 32 7.73 Mbp
100 186 1.10 Mbp 71 1.83 Mbp
1.090x 537 1.37 Gbp 361 1.38 Gbp
NG based on genome size 1.26 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 4 September 2024
bCopSec1.HiC.hap2.20240904.fasta.gz (287.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 26.41 Mbp 1 151.25 Mbp
20 9 20.72 Mbp 2 113.46 Mbp
30 15 17.32 Mbp 4 73.06 Mbp
40 23 13.67 Mbp 5 72.42 Mbp
50 34 9.68 Mbp 8 37.04 Mbp
60 52 5.77 Mbp 13 19.10 Mbp
70 83 3.13 Mbp 20 14.18 Mbp
80 166 0.76 Mbp 48 1.71 Mbp
90 0 0
100 0 0
0.832x 393 1.05 Gbp 235 1.05 Gbp
NG based on genome size 1.26 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/bCopSec1.yml (view)
species: Copsychus sechellarum
specimen: bCopSec1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Copsychus_sechellarum/bCopSec1/assembly_vgp_HiC_2.0/bCopSec1.HiC.hap1.20240904.fasta.gz
hap2: s3://genomeark/species/Copsychus_sechellarum/bCopSec1/assembly_vgp_HiC_2.0/bCopSec1.HiC.hap2.20240904.fasta.gz
pretext_hap1: s3://genomeark/species/Copsychus_sechellarum/bCopSec1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bCopSec1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Copsychus_sechellarum/bCopSec1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bCopSec1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Copsychus_sechellarum/bCopSec1/assembly_vgp_HiC_2.0/evaluation/merqury_s2_trioqc/bCopSec1_png/
pacbio_read_dir: s3://genomeark/species/Copsychus_sechellarum/bCopSec1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Copsychus_sechellarum/bCopSec1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Copsychus_sechellarum/bCopSec1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.9+galaxy0)
  - solve (3.7.0+galaxy3)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of bCopSec1, resulting in two complete haplotypes. The HiC prep kit used was the Swift-IDT kit. The assembly was performed on the VGL Galaxy instance. There is trio phasing data available for this individual (bCopSec2 and bCopSec3), but the trio-phased assembly performed worse relative to the HiC-phased assembly. 
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.