Phlebotomus perniciosus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 September 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 September 2025.
Assemblies
Individual 3 Mitochondrial Assembly
Version assembly_MT_rockefeller from 20 August 2025
idPhlPern3.MT.20250820.fasta.gz (4.8 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_standard_2.0/idPhlPern3.yml (view)
species: Phlebotomus perniciosus
specimem: idPhlPern3
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: false
hap1: s3://genomeark/species/Phlebotomus_perniciosus/idPhlPern3/assembly_vgp_standard_2.0/idPhlPern3.standard.hap1.20250821.fasta.gz
hap2: only primary assembly
pretext_hap1: s3://genomeark/species/Phlebotomus_perniciosus/idPhlPern3/assembly_vgp_standard_2.0/evaluation/hap1/pretext/s2/
pretext_hap2: only primary assembly
kmer_spectra_img: s3://genomeark/species/Phlebotomus_perniciosus/idPhlPern3/assembly_vgp_standard_2.0/evaluation/merqury/idPhlPern3_png/
pacbio_read_dir: s3://genomeark/species/Phlebotomus_perniciosus/idPhlPern3/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Phlebotomus_perniciosus/idPhlPern4/genomic_data/arima/
pipeline:
  - hifiasm (3.2.3+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - mitoHiFi (3.2.3+galaxy0) with invertebrate genetic code
  - VGP1 genomic profiling workflow (v0.3)
  - VGP4 HiFi HiC assembly workflow (v0.3.2)
  - VGP6 Purge_dups workflow (v0.10.2)
  - VGP8 HiC scaffolding workflow (v2.0) using HiC data from a different individual idPhlPern4
  - VGP9 decontamination workflow (v0.7) with database PlusPF 2022
  - Pre-curation worklfow (v1.0beta6)
notes: This was a Hifiasm primary assembly of idPhlPern3. Both primary and alternate assemblies were ran through VGP6 purge_dups workflow. The primary assembly was then scaffolded using HiC data from a different individual idPhlPern4. The HiC data were generated using the Arima v2 library prep kit, and require trimming before use. Please trim the first 5 bp off from the 5' end of both read files. The restriction enzymes used were the Arima v2 kit, so the cutting sites are GATC, GANTC, CTNAG, TTAA.
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.