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snakemake
README.md
conda_env.yaml
conda_env_latest.yaml
workflow_sarscov2.png
README.md

SARS CoV2

Tools

  • SRA-Toolkit
  • seqtk (bioconda)
  • snakemake (snakemake)
  • QC : fastqc/ fastp (bioconda)
  • Mapping : bowtie2 / bwa (bioconda)
  • Variant calling : GATK, samtools (bioconda)
  • Annotation : SnpEff (bioconda)
  • Phylogenetic tree : ...
  • ...

Environment

Copy the file conda_env.yaml into the no_backup folder of your home directory and then use following code to create the environment: mamba env create -f conda_env.yaml

Folder Structure (sars-cov2)

  • Snakemake_file
  • SRA_Toolkit -- fastq
  • Qc -- fastqc -- multiqc
  • Trimmgalore
  • mapping -- bowtie2 -- bwa

samples