Pulsatrix perspicillata

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bPulPer1 109.44 Gbp N/A 47.5 GiB
PacBio HiFi (.bam) bPulPer1 1003.25 Gbp N/A 435.5 GiB
Arima bPulPer1 127.43 Gbp N/A 60.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 19 March 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bPulPer1 PacBio HiFi (.fq) 109.44 Gbp N/A 47.5 GiB
PacBio HiFi (.bam) 1003.25 Gbp N/A 435.5 GiB
Arima 127.43 Gbp N/A 60.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 19 March 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 6 March 2024
bPulPer1.HiC.hap1.20240306.fasta.gz (485.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 7 25.15 Mbp 2 137.18 Mbp
20 18 17.80 Mbp 4 135.86 Mbp
30 33 12.83 Mbp 6 64.27 Mbp
40 53 9.70 Mbp 10 30.53 Mbp
50 83 5.83 Mbp 20 17.45 Mbp
60 133 3.45 Mbp 43 5.46 Mbp
70 223 1.80 Mbp 112 2.26 Mbp
80 415 0.79 Mbp 280 0.85 Mbp
90 1111 133.83 Kbp 923 139.83 Kbp
100 6136 11.45 Kbp 5891 11.45 Kbp
1.000x 6136 2.27 Gbp 5891 2.27 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 6 March 2024
bPulPer1.HiC.hap2.20240306.fasta.gz (389.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 30.33 Mbp 1 318.13 Mbp
20 10 23.83 Mbp 1 318.13 Mbp
30 17 19.94 Mbp 3 134.58 Mbp
40 26 17.07 Mbp 4 99.46 Mbp
50 37 11.92 Mbp 6 62.02 Mbp
60 53 8.14 Mbp 9 25.14 Mbp
70 77 5.06 Mbp 17 13.82 Mbp
80 125 2.44 Mbp 43 3.24 Mbp
90 258 493.40 Kbp 147 0.59 Mbp
100 2497 11.14 Kbp 2330 11.14 Kbp
1.000x 2497 1.57 Gbp 2330 1.57 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 6 March 2024
bPulPer1.MT.20240306.fasta.gz (5.8 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bPulPer1.yml (view)
species: Pulsatrix perspicillata
specimen: bPulPer1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Pulsatrix_perspicillata/bPulPer1/assembly_vgp_HiC_2.0/bPulPer1.HiC.hap1.20240306.fasta.gz
hap2: s3://genomeark/species/Pulsatrix_perspicillata/bPulPer1/assembly_vgp_HiC_2.0/bPulPer1.HiC.hap2.20240306.fasta.gz
pretext_hap1: s3://genomeark/species/Pulsatrix_perspicillata/bPulPer1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bPulPer1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Pulsatrix_perspicillata/bPulPer1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bPulPer1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Pulsatrix_perspicillata/bPulPer1/assembly_vgp_HiC_2.0/evaluation/merqury/bPulPer1_png/
pacbio_read_dir: s3://genomeark/species/Pulsatrix_perspicillata/bPulPer1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Pulsatrix_perspicillata/bPulPer1/genomic_data/arima/
mito: s3://genomeark/species/Pulsatrix_perspicillata/bPulPer1/assembly_MT_rockefeller/bPulPer1.MT.20240306.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of bPulPer1, 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. This assembly has a large amount of what seem to be fragmented repeat contigs. The estimated genome size from GenomeScope is 1.57Gbp, but hap1 contigs end up 2.27Gbp and hap2 contigs are 1.57Gbp, so a lot of the repeats seem to be retained in hap1. I say that they are repeats because running purge_dups resulted in a large fraction of hap1 being removed (~300Mbp) and labelled as REPEAT by purge_dups, but the assembly is still larger than expected (1.92Gbp). I have opted to not remove these repeats, and the unpurged assemblies were carried through to scaffolding, in favor of keeping these sequences. Nucmer against Strix aluco shows a good amount of colinearity among the larger scaffolds in the end, and the smaller fragments hitting against some un-named parts of S. aluco. Just a heads up! 
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.