Dermanura phaeotis

pygmy fruit-eating bat

Included in the VGP and BAT1K.

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


metadata.yaml (view) (edit on github)
species:
  name: Dermanura phaeotis
  short_name: mDerPha
  taxon_id: 1051665
  common_name: pygmy fruit-eating bat
  order:
    name: Chiroptera
  family:
    name: Natalidae
  individuals:
  - ''
  genome_size: 2489010000
  genome_size_method: GoaT
  project: [ vgp , bat1k ]
No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mDerPha1 105.45 Gbp 42.37x 79.7 GiB
PacBio HiFi (.bam) mDerPha1 105.10 Gbp 42.23x 359.9 GiB
Arima mDerPha1 154.30 Gbp 61.99x 85.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.49 Gbp.
Last upload on 19 April 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mDerPha1 PacBio HiFi (.fq) 105.45 Gbp 42.37x 79.7 GiB
PacBio HiFi (.bam) 105.10 Gbp 42.23x 359.9 GiB
Arima 154.30 Gbp 61.99x 85.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.49 Gbp.
Last upload on 19 April 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 21 April 2024
mDerPha1.HiC.hap1.20240421.fasta.gz (621.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 130.49 Mbp 2 214.48 Mbp
20 5 98.99 Mbp 3 191.28 Mbp
30 7 71.58 Mbp 4 179.79 Mbp
40 11 62.71 Mbp 5 174.01 Mbp
50 16 51.18 Mbp 7 139.64 Mbp
60 21 37.47 Mbp 9 127.78 Mbp
70 28 30.27 Mbp 11 110.21 Mbp
80 40 15.81 Mbp 14 57.58 Mbp
90 0 0
100 0 0
0.873x 256 2.17 Gbp 211 2.17 Gbp
NG based on genome size 2.49 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 21 April 2024
mDerPha1.HiC.hap2.20240421.fasta.gz (608.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 148.19 Mbp 2 211.91 Mbp
20 4 139.83 Mbp 3 193.94 Mbp
30 6 113.59 Mbp 4 181.61 Mbp
40 8 101.51 Mbp 5 173.32 Mbp
50 11 71.98 Mbp 7 148.08 Mbp
60 15 59.09 Mbp 9 128.26 Mbp
70 20 37.10 Mbp 11 110.73 Mbp
80 31 13.91 Mbp 14 54.95 Mbp
90 0 0
100 0 0
0.856x 211 2.13 Gbp 176 2.13 Gbp
NG based on genome size 2.49 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 21 April 2024
mDerPha1.MT.20240421.fasta.gz (561.5 MiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mDerPha1.yml (view)
species: Dermanura phaeotis
specimen: mDerPha1
projects: 
  - vgp
assembled_by_group: Rockefeller
combine_for_curation: true
hap1: s3://genomeark/species/Dermanura_phaeotis/mDerPha1/assembly_vgp_HiC_2.0/mDerPha1.HiC.hap1.20240421.fasta.gz
hap2: s3://genomeark/species/Dermanura_phaeotis/mDerPha1/assembly_vgp_HiC_2.0/mDerPha1.HiC.hap2.20240421.fasta.gz
pretext_hap1: s3://genomeark/species/Dermanura_phaeotis/mDerPha1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mDerPha1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Dermanura_phaeotis/mDerPha1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mDerPha1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Dermanura_phaeotis/mDerPha1/assembly_vgp_HiC_2.0/evaluation/merqury/mDerPha1_png/
pacbio_read_dir: s3://genomeark/species/Dermanura_phaeotis/mDerPha1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Dermanura_phaeotis/mDerPha1/genomic_data/arima/
mito: s3://genomeark/species/Dermanura_phaeotis/mDerPha1/assembly_MT_rockefeller/mDerPha1.MT.20240421.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - purge_dups (1.2.6+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of mDerPha1, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Swift-IDT. 
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.