2020.11.30【读书笔记】丨在本地运行NCBI细菌基因组注释工具（PGAP）

• Annotation in the biological analysis workflow
  • importance of gene annotation in whole-genome analyses
    • 
  • PGAP in brief
    • automated pipeline
    • Protein-coding gene prediction
      • protein homology
      • Ab initio calls
      • Hidden Markov Model
    • non-coding gene prediction
      • tRNAscan-SE
      • RFAM
      • Homology
    • functional annotation
      • Hidden Markov Models
      • BlastRules
      • CDD architectures
      • Protein homology
    • 
  • Why run PGAP yourself
    • QC
    • Quick
    • Large volume
    • compresion to Refseq
    • pipeline
• what is stand-alone PGAP
  • Goals for stand-alone PGAP
  • From PGAP at NCBI to stand-alone PGAP
  • How is stand-alone PGAP packaged
  • Hardware and software requirements
• Start-to-finish annotation
  • Download pgap.py
  • Dowdload the Docker image and reference data
  • Prepare the inputs
    • input file format
    • FASTA
    • Metadata
  • Run the annotation in the container
    • Execution of PGAP in a container
  • Review the results
    • output formats
      • FASTA
      • GFF
      • ASN.1
      • GenBank
    • Metadata
      • Topology
      • Species
      • Submitter
      • Submitter info
    • Annotation summary
      • Run information
      • Many frameshifts
• PGAP on 'preliminary assembly'
• Features in the works