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_curated from 21 November 2025
bCopSec1.hap1.cur.20251121.fasta.gz (347.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 44.49 Mbp 1 157.11 Mbp
20 7 26.28 Mbp 2 121.78 Mbp
30 12 21.51 Mbp 3 114.47 Mbp
40 18 18.41 Mbp 5 78.03 Mbp
50 26 14.53 Mbp 6 76.74 Mbp
60 35 10.43 Mbp 9 41.23 Mbp
70 51 6.78 Mbp 12 32.21 Mbp
80 73 4.67 Mbp 17 22.50 Mbp
90 107 2.84 Mbp 24 16.21 Mbp
100 177 1.15 Mbp 41 4.12 Mbp
1.097x 547 1.38 Gbp 315 1.39 Gbp
NG based on genome size 1.26 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 21 November 2025
bCopSec1.hap2.cur.20251121.fasta.gz (259.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 26.37 Mbp 1 155.54 Mbp
20 9 20.72 Mbp 2 115.06 Mbp
30 15 17.27 Mbp 3 113.46 Mbp
40 23 12.80 Mbp 5 71.94 Mbp
50 35 9.41 Mbp 7 39.28 Mbp
60 54 5.52 Mbp 12 22.23 Mbp
70 88 2.70 Mbp 19 14.95 Mbp
80 186 0.51 Mbp 37 3.08 Mbp
90 0 0
100 0 0
0.824x 409 1.04 Gbp 191 1.04 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.