Dixiphia pipra

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bDixPip1 541.01 Gbp N/A 0.9 TiB
PacBio HiFi (.fq) bDixPip1 57.22 Gbp N/A 41.8 GiB
PacBio HiFi (.bam) bDixPip1 100.02 Gbp N/A 221.7 GiB
Arima bDixPip1 90.65 Gbp N/A 48.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 15 August 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bDixPip1 PacBio HiFi (subreads) 541.01 Gbp N/A 0.9 TiB
PacBio HiFi (.fq) 57.22 Gbp N/A 41.8 GiB
PacBio HiFi (.bam) 100.02 Gbp N/A 221.7 GiB
Arima 90.65 Gbp N/A 48.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 15 August 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 7 July 2023
bDixPip1.hap1.cur.20230707.fasta.gz (333.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 38.48 Mbp 1 156.03 Mbp
20 9 19.71 Mbp 2 119.61 Mbp
30 15 16.98 Mbp 3 116.97 Mbp
40 22 14.54 Mbp 4 76.48 Mbp
50 32 10.45 Mbp 6 75.01 Mbp
60 44 7.54 Mbp 8 65.73 Mbp
70 62 5.56 Mbp 10 37.70 Mbp
80 91 3.09 Mbp 15 21.40 Mbp
90 148 1.28 Mbp 21 12.86 Mbp
100 1019 1.00 Kbp 696 1.00 Kbp
1.000x 1019 1.17 Gbp 696 1.17 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 16 January 2024
bDixPip1.hap2.cur.20240116.fasta.gz (293.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 30.72 Mbp 1 156.44 Mbp
20 7 20.33 Mbp 2 120.04 Mbp
30 13 17.57 Mbp 3 117.35 Mbp
40 19 14.40 Mbp 4 76.19 Mbp
50 28 11.12 Mbp 5 75.99 Mbp
60 39 7.20 Mbp 7 40.39 Mbp
70 56 4.83 Mbp 9 31.95 Mbp
80 82 3.27 Mbp 14 21.07 Mbp
90 127 1.38 Mbp 20 11.87 Mbp
100 902 1.00 Kbp 595 1.00 Kbp
1.000x 902 1.03 Gbp 595 1.03 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 13 February 2023
bDixPip1.MT.20230213.fasta.gz (5.5 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bDixPip1.yaml (view)
species: Dixiphia pipra
specimen: bDixPip1
projects: 
  - vgp
hap1: s3://genomeark/species/Dixiphia_pipra/bDixPip1/assembly_vgp_HiC_2.0/bDixPip1.HiC.hap1.20221214.fasta.gz
hap2: s3://genomeark/species/Dixiphia_pipra/bDixPip1/assembly_vgp_HiC_2.0/bDixPip1.HiC.hap2.20221214.fasta.gz
pretext_hap1: s3://genomeark/species/Dixiphia_pipra/bDixPip1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bDixPip1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Dixiphia_pipra/bDixPip1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bDixPip1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Dixiphia_pipra/bDixPip1/assembly_vgp_HiC_2.0/evaluation/merqury/bDixPip1_png/
pacbio_read_dir: s3://genomeark/species/Dixiphia_pipra/bDixPip1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Dixiphia_pipra/bDixPip1/genomic_data/arima/
hic_kit: Arima2
pipeline:
  - hifiasm (0.16.1+galaxy3)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of bDixPip1, resulting in two complete haplotypes. This individual did not have bionano data. HiC scaffolding was performed with YAHS. The kmer spectra indicates a heterogametic specimen. Becuase the sex chromosomes are split between the two haplotypes, we are including the file paths for both haplotypes in this single ticket. This assembly was done by Cassidy Johnson.
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.