Genome Analysis

To set environmental variables, edit the file set_variables.sh, and run:

source set_variables.sh

The folder names in this repository are prefixed with a number to indicate where its content is located in the pipeline: a lower number means earlier in the pipeline and a higher number means later in the pipeline. For example, the scripts in the folder 2_Mapped will depend on the the folders starting wih 0 and 1 to varying dregrees but not at all on the folders starting with numbers 3 and above.

The Pipeline

The the pipeline is described broadly here. See individual folders for detailed instructions.

Going from raw data to basic population genetics

This part currently only focuses on the mapping strategy (using a reference genome).

1. Put your raw fastq-files in the folder 0_Raw_data and your reference genome in the folder 0_Reference.
2. Index your reference using the script in the folder 0_Reference.
3. Filter your samples using the script in the folder 1_Pre_analysis.
4. Assemble your filtered reads and create BAM files by mapping to your reference genome using the script in the folder 2_Mapped.
5. Call variants and create a VCF file from the BAM files using a script in the folder 3_Call_variants.
6. Filter the VCF file using a different script in the folder 3_Call_variants.
7. Perform population genetic analyses of choice using the subdirectories of 4_Popgen.