GrENE-net pool seq pipeline

This repository contains the code necessary to run the genome-wide allele frequency estimation from the data produced by grene-net.org consortium.

Pipeline steps

SOFTWARE	TASK
skewer	Trimming & quality filter
fastqc	Visualize quality measurements
Bwa mem	Mapping to reference
Samtools	Alignment
IGV	Visualize alignment
bamfreq	Extract base counts per position
pool	Read two or more base count files and generate a fvcf

All steps up until pool are wrapped in the script grenepool.py which is awared of output files and, if the run failed, would start from the last keystone intermediate file unless forced.

Get the code

git clone https://github.com/MoisesExpositoAlonso/grenepool
cd grenepool
make

# to prompt help from the two main programs
./grenepool
./pool

To run analyses

./grenepool.py <yourfile.fastq.gz> 
./pool <outputname> <file1.freq> <file2.freq> ...

TO DO!

Probabilistic model to get frequency and estimate changes in time. Two previous softares options might be CLEAR or PoPoolation.