Platyrrhinus helleri

Heller's broad-nosed bat

Included in the VGP and BAT1K.

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


metadata.yaml (view) (edit on github)
species:
  short_name: mPlaHel
  name: Platyrrhinus helleri
  taxon_id: 27658
  common_name: Heller's broad-nosed bat
  order:
    name: Chiroptera
  family:
    name: Phyllostomidae
  individuals:
    - short_name: mPlaHel1
  genome_size: 2572140000
  genome_size_method: GoaT
  project: [ vgp , bat1k ]
No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mPlaHel1 18.38 Gbp 7.14x 63.5 GiB
PacBio HiFi (.bam) mPlaHel1 82.18 Gbp 31.95x 284.0 GiB
Arima mPlaHel1 144.57 Gbp 56.21x 80.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.57 Gbp.
Last upload on 23 November 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mPlaHel1 PacBio HiFi (.fq) 18.38 Gbp 7.14x 63.5 GiB
PacBio HiFi (.bam) 82.18 Gbp 31.95x 284.0 GiB
Arima 144.57 Gbp 56.21x 80.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.57 Gbp.
Last upload on 23 November 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 30 November 2023
mPlaHel1.HiC.hap1.20231130.fasta.gz (642.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 122.72 Mbp 1 245.53 Mbp
20 4 83.81 Mbp 2 214.00 Mbp
30 7 65.04 Mbp 4 179.29 Mbp
40 11 55.88 Mbp 5 171.41 Mbp
50 16 49.39 Mbp 6 151.72 Mbp
60 21 33.33 Mbp 8 142.18 Mbp
70 29 25.77 Mbp 10 128.24 Mbp
80 39 19.20 Mbp 11 118.47 Mbp
90 53 10.91 Mbp 14 60.87 Mbp
100 488 16.90 Kbp 429 16.90 Kbp
1.000x 488 2.27 Gbp 429 2.27 Gbp
NG based on genome size 2.57 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 30 November 2023
mPlaHel1.HiC.hap2.20231130.fasta.gz (611.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 81.96 Mbp 1 247.08 Mbp
20 6 73.52 Mbp 2 214.89 Mbp
30 9 63.67 Mbp 3 193.26 Mbp
40 12 58.30 Mbp 5 172.83 Mbp
50 16 47.66 Mbp 6 157.59 Mbp
60 21 42.57 Mbp 7 150.20 Mbp
70 27 30.93 Mbp 9 130.81 Mbp
80 37 18.37 Mbp 11 108.39 Mbp
90 50 13.49 Mbp 13 61.95 Mbp
100 368 16.44 Kbp 313 16.44 Kbp
1.000x 368 2.15 Gbp 313 2.15 Gbp
NG based on genome size 2.57 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 4 December 2023
mPlaHel1.MT.20231204.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mPlaHel1.yml (view)
species: Platyrrhinus helleri
specimen: mPlaHel1
projects: 
  - vgp
  - bat1k
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
primary: s3://genomeark/species/Platyrrhinus_helleri/mPlaHel1/assembly_vgp_HiC_2.0/mPlaHel1.HiC.hap1.20231130.fasta.gz
haplotigs: s3://genomeark/species/Platyrrhinus_helleri/mPlaHel1/assembly_vgp_HiC_2.0/mPlaHel1.HiC.hap2.20231130.fasta.gz
pretext: s3://genomeark/species/Platyrrhinus_helleri/mPlaHel1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mPlaHel1_hap1_s2.pretext
pretext: s3://genomeark/species/Platyrrhinus_helleri/mPlaHel1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mPlaHel1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Platyrrhinus_helleri/mPlaHel1/assembly_vgp_HiC_2.0/evaluation/merqury/mPlaHel1_png/
pacbio_read_dir: s3://genomeark/species/Platyrrhinus_helleri/mPlaHel1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Platyrrhinus_helleri/mPlaHel1/genomic_data/arima/
mito: s3://genomeark/species/Platyrrhinus_helleri/mPlaHel1/assembly_MT_rockefeller/mPlaHel1.MT.20231204.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of mPlaHel1. This hap1 assembly and hap2 assembly underwent separate HiC scaffolding with YaHS. The HiC prep kit used was Swift-IDT. The HiC reaction was using Arima kit v2.
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.