Agelaius phoeniceus

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CC BY-SA 3.0 Walter Siegmund (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bAgePho1 1538.85 Gbp N/A 2.6 TiB
PacBio HiFi (.fq) bAgePho1 85.05 Gbp N/A 70.2 GiB
PacBio HiFi (.bam) bAgePho1 220.56 Gbp N/A 761.6 GiB
Arima bAgePho1 76.71 Gbp N/A 38.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 14 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bAgePho1 PacBio HiFi (subreads) 1538.85 Gbp N/A 2.6 TiB
PacBio HiFi (.fq) 85.05 Gbp N/A 70.2 GiB
PacBio HiFi (.bam) 220.56 Gbp N/A 761.6 GiB
Arima 76.71 Gbp N/A 38.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 14 June 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 28 May 2024
bAgePho1.HiC.hap1.20240528.fasta.gz (307.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 94.47 Mbp 1 156.56 Mbp
20 3 63.05 Mbp 2 118.04 Mbp
30 5 49.53 Mbp 3 116.76 Mbp
40 8 37.34 Mbp 4 74.45 Mbp
50 11 30.09 Mbp 6 65.43 Mbp
60 15 21.06 Mbp 8 38.33 Mbp
70 21 17.85 Mbp 11 23.37 Mbp
80 29 11.05 Mbp 17 15.93 Mbp
90 44 4.41 Mbp 27 7.67 Mbp
100 478 20.17 Kbp 331 20.17 Kbp
1.000x 478 1.11 Gbp 331 1.11 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 28 May 2024
bAgePho1.HiC.hap2.20240528.fasta.gz (345.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 62.68 Mbp 1 153.85 Mbp
20 4 56.96 Mbp 2 118.82 Mbp
30 6 52.59 Mbp 3 118.42 Mbp
40 9 38.69 Mbp 5 74.23 Mbp
50 12 29.99 Mbp 7 64.25 Mbp
60 18 19.75 Mbp 9 42.37 Mbp
70 25 16.54 Mbp 13 21.86 Mbp
80 36 8.06 Mbp 20 14.55 Mbp
90 57 3.85 Mbp 33 6.46 Mbp
100 465 18.52 Kbp 317 18.52 Kbp
1.000x 465 1.27 Gbp 317 1.27 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 30 May 2024
bAgePho1.MT.20240530.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bAgePho1.yml (view)
species: Agelaius phoeniceus
specimen: bAgePho1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Agelaius_phoeniceus/bAgePho1/assembly_vgp_HiC_2.0/bAgePho1.HiC.hap1.20240528.fasta.gz
hap2: s3://genomeark/species/Agelaius_phoeniceus/bAgePho1/assembly_vgp_HiC_2.0/bAgePho1.HiC.hap2.20240528.fasta.gz
pretext_hap1: s3://genomeark/species/Agelaius_phoeniceus/bAgePho1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bAgePho1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Agelaius_phoeniceus/bAgePho1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bAgePho1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Agelaius_phoeniceus/bAgePho1/assembly_vgp_HiC_2.0/evaluation/merqury/bAgePho1_png/
pacbio_read_dir: s3://genomeark/species/Agelaius_phoeniceus/bAgePho1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Agelaius_phoeniceus/bAgePho1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Agelaius_phoeniceus/bAgePho1/genomic_data/arima/
mito: s3://genomeark/species/Agelaius_phoeniceus/bAgePho1/assembly_MT_rockefeller/bAgePho1.MT.20240530.fasta.gz
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - solve (3.7)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of bAgePho1, resulting in two complete haplotypes. This sample had Bionano. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Swift-IDT library prep. 
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.