Population mapping pipeline is now available

The pipeline to map the reads from several samples to a (reference) genome is now available. As input it takes a .fasta file of a reference genome, and one or more paths to directories that contain reads. The pipeline will go through every subdirectory of the path you gave as input and search for files with .fq.gz extension. This means that you can give a path to a directory that has several subdirectories with reads. See example:

/lustre/nobackup/WUR/ABGC/shared/Chicken/Africa/X201SC20031230-Z01-F006_multipath  
├── X201SC20031230-Z01-F006_1  
│   └── raw_data  
│       ├── a109_26_15_1_H  
│       │   ├── a109_26_15_1_H_FDSW202597655-1r_HWFFFDSXY_L3_1.fq.gz  
│       │   ├── a109_26_15_1_H_FDSW202597655-1r_HWFFFDSXY_L3_2.fq.gz  
│       │   └── MD5.txt  
│       └── a20_10_16_1_H  
│           ├── a20_10_16_1_H_FDSW202597566-1r_HWFFFDSXY_L3_1.fq.gz  
│           ├── a20_10_16_1_H_FDSW202597566-1r_HWFFFDSXY_L3_2.fq.gz  
│           └── MD5.txt  
└── X201SC20031230-Z01-F006_2  
    └── raw_data  
        ├── a349_Be_17_1_C  
        │   ├── a349_Be_17_1_C_FDSW202597895-1r_HWFFFDSXY_L3_1.fq.gz  
        │   ├── a349_Be_17_1_C_FDSW202597895-1r_HWFFFDSXY_L3_2.fq.gz  
        │   └── MD5.txt  
        └── a360_Be_05_1_H  
            ├── a360_Be_05_1_H_FDSW202597906-1r_HWFFFDSXY_L3_1.fq.gz  
            ├── a360_Be_05_1_H_FDSW202597906-1r_HWFFFDSXY_L3_2.fq.gz  
            └── MD5.txt  

In this case, since the path given was path1: /lustre/nobackup/WUR/ABGC/shared/Chicken/Africa/X201SC20031230-Z01-F006_multipath, then all these read files will be used in the pipeline.

The output of this pipeline is the mapped reads per sample - in sorted and indexed .bam files and a qualimap report for each sample, as well as a table with a summary of Mean coverage, Mapping rate, and Mean mapping quality for all the samples

You can find the description here. There you can also find the tools that the pipeline uses and the output. The pipeline can be found here.

To use it, first follow the instructions on running my snakemake pipelines.