Caloenas nicobarica

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bCalNic1 81.63 Gbp N/A 39.1 GiB
PacBio HiFi (.bam) bCalNic1 706.42 Gbp N/A 338.3 GiB
Arima bCalNic1 114.95 Gbp N/A 60.8 GiB
Dovetail Genomics bCalNic1 55.44 Gbp N/A 29.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 8 January 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bCalNic1 PacBio HiFi (.fq) 81.63 Gbp N/A 39.1 GiB
PacBio HiFi (.bam) 706.42 Gbp N/A 338.3 GiB
Arima 114.95 Gbp N/A 60.8 GiB
Dovetail Genomics 55.44 Gbp N/A 29.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 8 January 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 10 July 2023
bCalNic1.hap1.cur.20230710.fasta.gz (349.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 68.65 Mbp 1 216.43 Mbp
20 4 57.55 Mbp 2 165.86 Mbp
30 6 48.27 Mbp 3 122.86 Mbp
40 10 29.20 Mbp 4 110.15 Mbp
50 14 25.10 Mbp 5 79.70 Mbp
60 20 20.58 Mbp 7 42.83 Mbp
70 27 14.86 Mbp 10 24.86 Mbp
80 38 9.29 Mbp 16 17.70 Mbp
90 68 1.48 Mbp 32 3.55 Mbp
100 923 15.01 Kbp 806 16.52 Kbp
1.000x 923 1.29 Gbp 806 1.29 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 10 July 2023
bCalNic1.hap2.cur.20230710.fasta.gz (315.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 54.22 Mbp 1 215.72 Mbp
20 4 48.12 Mbp 2 165.54 Mbp
30 7 42.79 Mbp 2 165.54 Mbp
40 10 28.60 Mbp 3 123.28 Mbp
50 15 24.69 Mbp 4 107.99 Mbp
60 20 22.24 Mbp 6 70.09 Mbp
70 26 18.04 Mbp 8 40.86 Mbp
80 34 11.98 Mbp 13 22.98 Mbp
90 47 5.43 Mbp 20 11.98 Mbp
100 344 15.18 Kbp 226 15.18 Kbp
1.000x 344 1.20 Gbp 226 1.20 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 10 July 2023
bCalNic1.MT.20230710.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bCalNic1_hap1.yml (view)
species: Caloenas nicobarica
specimen: bCalNic1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Caloenas_nicobarica/bCalNic1/assembly_vgp_HiC_2.0/bCalNic1.HiC.hap1.20230710.fasta.gz
hap2: s3://genomeark/species/Caloenas_nicobarica/bCalNic1/assembly_vgp_HiC_2.0/bCalNic1.HiC.hap2.20230710.fasta.gz
pretext_hap1: s3://genomeark/species/Caloenas_nicobarica/bCalNic1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bCalNic1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Caloenas_nicobarica/bCalNic1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bCalNic1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Caloenas_nicobarica/bCalNic1/assembly_vgp_HiC_2.0/evaluation/merqury/bCalNic1_png/
pacbio_read_dir: s3://genomeark/species/Caloenas_nicobarica/bCalNic1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Caloenas_nicobarica/bCalNic1/genomic_data/arima/
mito: s3://genomeark/species/Caloenas_nicobarica/bCalNic1/assembly_MT_rockefeller/bCalNic1.MT.20230710.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
  - mitohifi (3+galaxy0)
notes: This was a Hifiasm-HiC assembly of bCalNic1, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Arima library prep. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. 
assembly_vgp_HiC_2.0/bCalNic1_hap2.yml (view)
species: Caloenas nicobarica
specimen: bCalNic1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Caloenas_nicobarica/bCalNic1/assembly_vgp_HiC_2.0/bCalNic1.HiC.hap1.20230710.fasta.gz
hap2: s3://genomeark/species/Caloenas_nicobarica/bCalNic1/assembly_vgp_HiC_2.0/bCalNic1.HiC.hap2.20230710.fasta.gz
pretext_hap1: s3://genomeark/species/Caloenas_nicobarica/bCalNic1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bCalNic1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Caloenas_nicobarica/bCalNic1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bCalNic1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Caloenas_nicobarica/bCalNic1/assembly_vgp_HiC_2.0/evaluation/merqury/bCalNic1_png/
pacbio_read_dir: s3://genomeark/species/Caloenas_nicobarica/bCalNic1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Caloenas_nicobarica/bCalNic1/genomic_data/arima/
mito: s3://genomeark/species/Caloenas_nicobarica/bCalNic1/assembly_MT_rockefeller/bCalNic1.MT.20230710.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
  - mitohifi (3+galaxy0)
notes: This was a Hifiasm-HiC assembly of bCalNic1, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Arima library prep. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. 
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.