Columba livia

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bColLiv1 1288.41 Gbp N/A 2.2 TiB
PacBio HiFi (.fq) bColLiv1 62.13 Gbp N/A 49.9 GiB
PacBio HiFi (.bam) bColLiv1 185.15 Gbp N/A 651.7 GiB
Arima bColLiv1 122.66 Gbp N/A 63.0 GiB
Illumina bColLiv2 52.19 Gbp N/A 21.9 GiB
bColLiv3 59.25 Gbp N/A 25.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 1 August 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bColLiv1 PacBio HiFi (subreads) 1288.41 Gbp N/A 2.2 TiB
PacBio HiFi (.fq) 62.13 Gbp N/A 49.9 GiB
PacBio HiFi (.bam) 185.15 Gbp N/A 651.7 GiB
Arima 122.66 Gbp N/A 63.0 GiB
bColLiv2 Illumina 52.19 Gbp N/A 21.9 GiB
bColLiv3 Illumina 59.25 Gbp N/A 25.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 1 August 2024.
Assemblies
Individual 1 Merged Trio Assembly
Version assembly_curated from 6 February 2024
bColLiv1.pat.W.cur.20240206.fasta.gz (324.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 40.52 Mbp 1 212.39 Mbp
20 8 29.35 Mbp 2 163.73 Mbp
30 13 21.50 Mbp 3 122.09 Mbp
40 20 17.18 Mbp 4 84.82 Mbp
50 28 14.04 Mbp 6 68.98 Mbp
60 40 8.85 Mbp 8 41.45 Mbp
70 59 5.96 Mbp 13 22.35 Mbp
80 89 3.22 Mbp 20 14.04 Mbp
90 173 0.87 Mbp 44 1.55 Mbp
100 1118 12.90 Kbp 869 12.90 Kbp
1.000x 1118 1.33 Gbp 869 1.33 Gbp
NG based on genome size .
Individual 1 Maternal Assembly
Version assembly_curated from 6 February 2024
bColLiv1.mat.cur.20240206.fasta.gz (290.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 47.12 Mbp 1 212.75 Mbp
20 6 34.65 Mbp 2 160.37 Mbp
30 10 22.43 Mbp 2 160.37 Mbp
40 15 20.61 Mbp 3 121.99 Mbp
50 22 17.43 Mbp 5 68.65 Mbp
60 30 12.09 Mbp 7 39.94 Mbp
70 42 7.10 Mbp 11 22.43 Mbp
80 62 4.33 Mbp 17 14.46 Mbp
90 108 1.32 Mbp 36 2.79 Mbp
100 842 14.45 Kbp 650 15.17 Kbp
1.000x 842 1.18 Gbp 650 1.18 Gbp
NG based on genome size .
Individual 1 Paternal Assembly
No assembly available.


Contigs Scaffolds
NG LG Len LG Len
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0.000x - 0.0 Mbp - 0.0 Mbp
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 14 November 2023
bColLiv1.MT.20231114.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_trio_2.0/bColLiv1_hap1.yml (view)
species: Columba livia
specimen: bColLiv1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap1 (pat)
hap1 (pat): s3://genomeark/species/Columba_livia/bColLiv1/assembly_vgp_trio_2.0/evaluation/bColLiv1.trio.hap1.20231102.fasta.gz
hap2 (mat): s3://genomeark/species/Columba_livia/bColLiv1/assembly_vgp_trio_2.0/evaluation/bColLiv1.trio.hap2.20231102.fasta.gz
pretext_hap1: s3://genomeark/species/Columba_livia/bColLiv1/assembly_vgp_trio_2.0/evaluation/hap1/pretext/bColLiv1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Columba_livia/bColLiv1/assembly_vgp_trio_2.0/evaluation/hap2/pretext/bColLiv1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Columba_livia/bColLiv1/assembly_vgp_trio_2.0/evaluation/merqury/bColLiv1_png/
pacbio_read_dir:  s3://genomeark/species/Columba_livia/bColLiv1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Columba_livia/bColLiv1/genomic_data/arima/
mito: s3://genomeark/species/Columba_livia/bColLiv1/assembly_MT_rockefeller/bColLiv1.MT.20231114.fasta.gz
pipeline: 
        - Hifiasm + trio phasing 0.19.7 + galaxy1
        - purge_dups (1.2.6 + galaxy0)
        - yahs (1.2a.2 + galaxy0)
        - mitoHiFi (3.0 + galaxy0)
notes: This was a Hifiasm + trio assembly of bColLiv1, resulting in two complete haplotypes (maternal and paternal). 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. The order and orientation of scaffolds is uncertain in the W chromosome due to contiguity dropouts.
assembly_vgp_trio_2.0/bColLiv1_hap2.yml (view)
pecies: Columba livia
specimen: bColLiv1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap2 (mat)
hap1 (pat): s3://genomeark/species/Columba_livia/bColLiv1/assembly_vgp_trio_2.0/evaluation/bColLiv1.trio.hap1.20231102.fasta.gz
hap2 (mat): s3://genomeark/species/Columba_livia/bColLiv1/assembly_vgp_trio_2.0/evaluation/bColLiv1.trio.hap2.20231102.fasta.gz
pretext_hap1: s3://genomeark/species/Columba_livia/bColLiv1/assembly_vgp_trio_2.0/evaluation/hap1/pretext/bColLiv1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Columba_livia/bColLiv1/assembly_vgp_trio_2.0/evaluation/hap2/pretext/bColLiv1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Columba_livia/bColLiv1/assembly_vgp_trio_2.0/evaluation/merqury/bColLiv1_png/
pacbio_read_dir:  s3://genomeark/species/Columba_livia/bColLiv1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Columba_livia/bColLiv1/genomic_data/arima/
mito: s3://genomeark/species/Columba_livia/bColLiv1/assembly_MT_rockefeller/bColLiv1.MT.20231114.fasta.gz
pipeline: 
        - Hifiasm + trio phasing (0.19.7 + galaxy1)
        - yahs (1.2a.2 + galaxy0)
        - mitoHiFi (3.0 + galaxy0)
notes: This was a Hifiasm + trio assembly of bColLiv1, resulting in two complete haplotypes (maternal and paternal). 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.