Artibeus intermedius

intermediate 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:
  short_name: mArtInt
  name: Artibeus intermedius
  taxon_id: 51014
  common_name: intermediate fruit-eating bat
  order:
    name: Chiroptera
  family:
    name: Phyllostomidae
  individuals:
  - mArtInt1
  genome_size: 2376540000
  genome_size_method: GoaT
  project: [ vgp , bat1k ]
No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mArtInt1 95.37 Gbp 40.13x 74.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.38 Gbp.
Last upload on 6 November 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mArtInt1 PacBio HiFi (.fq) 95.37 Gbp 40.13x 74.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.38 Gbp.
Last upload on 6 November 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 11 September 2023
mArtInt1.hap1.cur.20230911.fasta.gz (651.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 123.32 Mbp 1 245.41 Mbp
20 4 98.74 Mbp 2 215.74 Mbp
30 7 87.30 Mbp 4 182.64 Mbp
40 10 65.88 Mbp 5 176.20 Mbp
50 14 60.03 Mbp 6 160.43 Mbp
60 18 51.00 Mbp 8 149.66 Mbp
70 23 35.76 Mbp 9 144.92 Mbp
80 30 29.62 Mbp 11 119.58 Mbp
90 41 16.80 Mbp 13 101.25 Mbp
100 500 8.48 Kbp 419 11.39 Kbp
1.000x 500 2.29 Gbp 419 2.29 Gbp
NG based on genome size 2.38 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 11 September 2023
mArtInt1.hap2.cur.20230911.fasta.gz (548.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 139.14 Mbp 1 244.72 Mbp
20 3 137.07 Mbp 2 215.03 Mbp
30 5 103.10 Mbp 3 200.04 Mbp
40 7 96.07 Mbp 4 180.18 Mbp
50 9 74.64 Mbp 6 167.57 Mbp
60 13 57.75 Mbp 7 149.72 Mbp
70 17 43.88 Mbp 8 141.47 Mbp
80 23 33.35 Mbp 10 121.43 Mbp
90 31 18.46 Mbp 12 98.81 Mbp
100 243 8.59 Kbp 187 10.83 Kbp
1.000x 243 2.08 Gbp 187 2.08 Gbp
NG based on genome size 2.38 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 28 February 2024
mArtInt1.MT.20240228.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mArtInt1_hap1.yml (view)
species: Artibeus intermedius
specimen: mArtInt1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Artibeus_intermedius/mArtInt1/assembly_vgp_HiC_2.0/mArtInt1.HiC.hap1.20230911.fasta.gz
hap2: s3://genomeark/species/Artibeus_intermedius/mArtInt1/assembly_vgp_HiC_2.0/mArtInt1.HiC.hap2.20230911.fasta.gz
pretext_hap1: s3://genomeark/species/Artibeus_intermedius/mArtInt1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mArtInt1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Artibeus_intermedius/mArtInt1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mArtInt1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Artibeus_intermedius/mArtInt1/assembly_vgp_HiC_2.0/evaluation/merqury/mArtInt1_png/
pacbio_read_dir: s3://genomeark/species/Artibeus_intermedius/mArtInt1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Artibeus_intermedius/mArtInt1/genomic_data/arima/
mito: s3://genomeark/species/Artibeus_intermedius/mArtInt1/assembly_MT_rockefeller/mArtInt1.MT.20240228.fasta.gz
pipeline: 
  - hifiasm (0.16.1+galaxy4)
  - yahs (1.2a.2+galaxy0)
notes: This was a Hifiasm-HiC assembly of mArtInt1, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Swift-IDT. 
assembly_vgp_HiC_2.0/mArtInt1_hap2.yml (view)
species: Artibeus intermedius
specimen: mArtInt1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Artibeus_intermedius/mArtInt1/assembly_vgp_HiC_2.0/mArtInt1.HiC.hap1.20230911.fasta.gz
hap2: s3://genomeark/species/Artibeus_intermedius/mArtInt1/assembly_vgp_HiC_2.0/mArtInt1.HiC.hap2.20230911.fasta.gz
pretext_hap1: s3://genomeark/species/Artibeus_intermedius/mArtInt1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mArtInt1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Artibeus_intermedius/mArtInt1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mArtInt1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Artibeus_intermedius/mArtInt1/assembly_vgp_HiC_2.0/evaluation/merqury/mArtInt1_png/
pacbio_read_dir: s3://genomeark/species/Artibeus_intermedius/mArtInt1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Artibeus_intermedius/mArtInt1/genomic_data/arima/
mito: s3://genomeark/species/Artibeus_intermedius/mArtInt1/assembly_MT_rockefeller/mArtInt1.MT.20240228.fasta.gz
pipeline: 
  - hifiasm (0.16.1+galaxy4)
  - yahs (1.2a.2+galaxy0)
notes: This was a Hifiasm-HiC assembly of mArtInt1, 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.