This is a repo that contains installers and snakemake scripts to execute the pipelines described by Kofler et al. in popoolation 1 and 2:
-
QC with Trimmomatic
-
Mapping with Bowtie2
-
BAM wrangling and SNP calling with samtools
-
Population measures with popoolation
-
Pairwise comparisons between populations with popoolation2
Follow the contents of the .travis.yml
file:
-
Clone and install the software
git clone https://github.com/jlanga/smsk_popoolation.git smsk_popoolation cd smsk_popoolation snakemake --use-conda --create-envs-only
-
Run the test dataset:
snakemake --use-conda -
-
Modify the following files:
-
features.yaml
: the path to the genome reference, and the names of every chromosome to be processed. -
samples.tsv
: paths and library information of each of the samples. -
params.yml
: execution parameters of different tools. -
cluster.json
: memory limits for some of the steps-
-
-
Execute the pipeline:
snakemake --use-conda -j