Anodorhynchus hyacinthinus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bAnoHya1 50.29 Gbp N/A 28.9 GiB
PacBio HiFi (.bam) bAnoHya1 376.35 Gbp N/A 216.0 GiB
Arima bAnoHya1 68.79 Gbp N/A 36.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 20 March 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bAnoHya1 PacBio HiFi (.fq) 50.29 Gbp N/A 28.9 GiB
PacBio HiFi (.bam) 376.35 Gbp N/A 216.0 GiB
Arima 68.79 Gbp N/A 36.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 20 March 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 21 December 2023
bAnoHya1.HiC.hap1.20231221.fasta.gz (315.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 54.47 Mbp 1 167.34 Mbp
20 5 36.95 Mbp 2 162.36 Mbp
30 8 33.72 Mbp 3 129.35 Mbp
40 12 30.00 Mbp 3 129.35 Mbp
50 16 23.42 Mbp 4 124.19 Mbp
60 22 15.33 Mbp 5 96.24 Mbp
70 30 10.72 Mbp 7 65.26 Mbp
80 43 5.96 Mbp 9 27.57 Mbp
90 71 2.67 Mbp 15 8.68 Mbp
100 554 14.23 Kbp 419 14.23 Kbp
1.000x 554 1.11 Gbp 419 1.11 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 21 December 2023
bAnoHya1.HiC.hap2.20231221.fasta.gz (357.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 57.03 Mbp 1 167.23 Mbp
20 6 32.44 Mbp 2 162.85 Mbp
30 10 30.14 Mbp 3 129.99 Mbp
40 15 22.30 Mbp 4 124.67 Mbp
50 22 17.96 Mbp 5 106.27 Mbp
60 30 14.39 Mbp 6 96.60 Mbp
70 42 7.95 Mbp 8 66.23 Mbp
80 64 4.89 Mbp 10 45.77 Mbp
90 105 1.89 Mbp 23 6.31 Mbp
100 628 14.29 Kbp 450 14.29 Kbp
1.000x 628 1.30 Gbp 450 1.30 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 5 January 2024
bAnoHya1.MT.20240105.fasta.gz (5.8 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bAnoHya1.yml (view)
species: Anodorhynchus hyacinthinus 
specimen: bAnoHya1 
projects:  
  - vgp 
  - gbb 
assembled_by_group: Rockefeller 
data_location: S3 
release_to: S3 
primary: s3://genomeark/species/Anodorhynchus_hyacinthinus/bAnoHya1/assembly_vgp_HiC_2.0/bAnoHya1.HiC.hap1.20231221.fasta.gz 
haplotigs: s3://genomeark/species/Anodorhynchus_hyacinthinus/bAnoHya1/assembly_vgp_HiC_2.0/bAnoHya1.HiC.hap2.20231221.fasta.gz 
pretext: s3://genomeark/species/Anodorhynchus_hyacinthinus/bAnoHya1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bAnoHya1_hap1_s2.pretext 
pretext: s3://genomeark/species/Anodorhynchus_hyacinthinus/bAnoHya1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bAnoHya1_hap2_s2.pretext 
kmer_spectra_img: s3://genomeark/species/Anodorhynchus_hyacinthinus/bAnoHya1/assembly_vgp_HiC_2.0/evaluation/merqury/bAnoHya1_png/ 
pacbio_read_dir: s3://genomeark/species/Anodorhynchus_hyacinthinus/bAnoHya1/genomic_data/pacbio_hifi/ 
pacbio_read_type: hifi 
hic_read_dir: s3://genomeark/species/Anodorhynchus_hyacinthinus/bAnoHya1/genomic_data/arima/ 
pipeline:  
  - hifiasm (0.16.1+galaxy4) 
  - yahs (1.2a.2+galaxy1) 
notes: This was a Hifiasm-HiC assembly of bAnoHya1. The hap1 assembly and hap2 assembly underwent separate HiC scaffolding with YaHS. The HiC prep kit used was Arima, so 5 bp were trimmed off the start of the Hi-C reads before scaffolding. 
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.