pal_filter

Program to pick optimum loci from the output of pal_finder_v0.02.04

This program can be used to filter output from pal_finder and choose the 'optimum' loci.

For the paper referencing this workflow, see Griffiths et al. 2016

To contact the author: (griffiths.sarahm@gmail.com)

INSTALLATION INSTRUCTIONS

To run pal_filter.py you will need the following:

Biopython (http://biopython.org/wiki/Download)

PANDAseq (https://github.com/neufeld/pandaseq)

Clone the pal_filter repo using your terminal:

git clone https://github.com/graemefox/pal_filter

Then move into the directory and allow execution of the script:

cd pal_filter/

chmod +x pal_filter.py

USAGE

You must supply pal_filter.py both your paired-end FastQ files (R1 and R2 files) and the output from pal_finder (the -i, -j and -p flags respectively).

You can then turn on the pal_filter.py filters using any of the flags below (we recommend using all flags for the best results in your PCR)

EXAMPLE USAGE

./pal_filter.py -i R1.fastq -j R2.fastq -p pal_finder_output.txt -primers -occurrences -rankmotifs -assembly

TROUBLESHOOTING

If when using the -assembly option you get an error message stating that "Assembly.fasta" does not exist, you do not have PANDAseq properly installed and in your $PATH. On Ubuntu, follow the installation instructions on https://github.com/neufeld/pandaseq to add the repository and install using aptitude.

REFERENCES

Girffiths, S.M., Fox, G., Briggs, P.J., Donaldson, I.J., Hood, S., Richardson, P., Leaver, G.W., Truelove, N.K., Preziosi, R.F. (2016) A Galaxy-based bioinformatics pipeline for optimised, streamlined microsatellite development from Illumina next-generation sequencing data. Conservation Genetics Resources. Vol. 8. Issue 4. pp. 481 - 486.