Pelecanus crispus

Dalmatian pelican

Included in the VGP.

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


metadata.yaml (view) (edit on github)
species:
  short_name: bPelCri
  name: Pelecanus crispus
  taxon_id: 36300
  common_name: Dalmatian pelican
  order:
    name: Pelecaniformes
  family:
    name: Pelecanidae
  individuals:
    - short_name: bPelCri1
  project: [ vgp ]
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bPelCri1 494.25 Gbp 375.98x 887.1 GiB
PacBio HiFi (.fq) bPelCri1 36.43 Gbp 27.71x 27.3 GiB
PacBio HiFi (.bam) bPelCri1 33.14 Gbp 25.21x 24.8 GiB
Bionano bPelCri1 N/A 1243.68x 1.7 GiB
Arima bPelCri2 88.86 Gbp 67.60x 44.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.31 Gbp.
Last upload on 6 February 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bPelCri1 PacBio HiFi (subreads) 494.25 Gbp 375.98x 887.1 GiB
PacBio HiFi (.fq) 36.43 Gbp 27.71x 27.3 GiB
PacBio HiFi (.bam) 33.14 Gbp 25.21x 24.8 GiB
Bionano N/A 1243.68x 1.7 GiB
bPelCri2 Arima 88.86 Gbp 67.60x 44.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.31 Gbp.
Last upload on 6 February 2023.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 27 May 2023
bPelCri1.pri.cur.20230527.fasta.gz (372.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 28.13 Mbp 1 227.93 Mbp
20 9 25.38 Mbp 2 176.27 Mbp
30 16 17.62 Mbp 2 176.27 Mbp
40 24 12.27 Mbp 3 133.47 Mbp
50 36 9.67 Mbp 5 86.81 Mbp
60 51 8.01 Mbp 6 85.03 Mbp
70 73 5.19 Mbp 8 52.02 Mbp
80 102 3.56 Mbp 11 43.80 Mbp
90 156 1.51 Mbp 16 18.73 Mbp
100 700 16.54 Kbp 310 16.54 Kbp
1.000x 700 1.31 Gbp 310 1.31 Gbp
NG based on genome size 1.31 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 27 May 2023
bPelCri1.alt.cur.20230527.fasta.gz (345.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 107 0.89 Mbp 107 0.89 Mbp
20 267 0.66 Mbp 267 0.66 Mbp
30 473 0.53 Mbp 473 0.53 Mbp
40 727 432.56 Kbp 727 432.56 Kbp
50 1036 352.77 Kbp 1036 352.77 Kbp
60 1425 275.78 Kbp 1425 275.78 Kbp
70 1929 206.07 Kbp 1929 206.07 Kbp
80 2631 142.63 Kbp 2631 142.63 Kbp
90 3766 74.57 Kbp 3766 74.57 Kbp
100 7284 8.19 Kbp 7284 8.19 Kbp
1.000x 7284 1.21 Gbp 7284 1.21 Gbp
NG based on genome size 1.31 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 7 April 2023
bPelCri1.MT.20230407.fasta.gz (5.7 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_standard_2.0/bPelCri1.yml (view)
species: Pelecanus crispus
specimen: bPelCri1
projects: 
  - vgp
data_location: S3
release_to: S3
primary: s3://genomeark/species/Pelecanus_crispus/bPelCri1/assembly_vgp_standard_2.0/bPelCri1.standard.pri.20230327.fasta.gz
haplotigs: s3://genomeark/species/Pelecanus_crispus/bPelCri1/assembly_vgp_standard_2.0/bPelCri1.standard.alt.20230327.fasta.gz
pretext: s3://genomeark/species/Pelecanus_crispus/bPelCri1/assembly_vgp_standard_2.0/evaluation/pri/pretext/bPelCri1_pri__s2.heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Pelecanus_crispus/bPelCri1/assembly_vgp_standard_2.0/evaluation/merqury/bPelCri1_png/
mito: s3://genomeark/species/Pelecanus_crispus/bPelCri1/assembly_MT_rockefeller/bPelCri1.MT.20230407.fasta.gz
pacbio_read_dir: s3://genomeark/species/Pelecanus_crispus/bPelCri1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Pelecanus_crispus/bPelCri1/genomic_data/arima/
pipeline:
  - hifiasm (0.18.8+galaxy1)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a primary/alternate assembly of bPelCri1, done using hifiasm with internal purging turned on to default level. This assembly did not use bionano data, and the HiC data came from another individual (bPelCri2). HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. There is bionano data available from external sequencing in the respective genomeark folder, but it was not used for this assembly.
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.