Viral genome notebook
  • Building consensus genome from raw fastq reads
    • Configure notebook for run
    • Prepare sample list
    • Load required python libraries
    • Fetch fastq files from SRA
      • Sub-sample reads for binder run
    • Check for viral DNA contamination using Fastv
      • Fetch required reference genomes and list of unique k-mers
      • Prepare function for fastv run
      • Run fastv for all samples
    • De-novo assembly of viral genome using Megahit
      • Prepare function for Megahit assembly run
      • Run de-novo assembly for all the samples
    • Map raw reads on reference genome
      • Prepare function for reference genome fetching
      • Build Bowtie2 index for reference genome
      • Prepare function for bowtie2 mapping
      • Run bowtie2 mapping for all the samples
    • Consensus genome building from mapped reads
      • Prepare function for consensus fasta building
      • Run consensus fasta building for all samples
  • Multiple sequence alignment and tree building
    • Data fetching
    • Multiple sequence alignment with Muscle
    • Tree building using FastTree
    • Plotting trees
    • Referenc
  • Tree building for 153 Coronavirus genomes
    • Fetch data
    • Build phylogenetic tree with FastTree
    • Plot trees
    • Reference
  • Alignment and tree building using Nextstrain
    • Introduction
    • Configure notebook for run
    • Load required python libraries
    • Fetch genome sequences
    • Multiple sequence alignment and tree building
    • Metadata configs for Nextstrain
    • Nextstrain visualization
    • References
Viral genome notebook
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