pseudogene/rad-scripts

Various RAD-seq related scripts

rad-scripts

We foster the openness, integrity, and reproducibility of scientific research.

Various scripts and tools to process RAD-sequences

Associated publication

under-submission

How to use this repository?

This repository host, various scripts and tools to process RAD-sequences. Feel free to adapt the scripts and tools, but remember to cite their authors!

To look at our scripts, browse through this repository. If you want to use some of the scripts, you will need to clone this repository. If you want to use our scripts for our own research, fork this repository and cite the authors.

Available scripts (so far)

• ddRAD_enzyme.pl: A very simple bioperl script predicting the distribution of the fragment length after a ddRAD.

#Download a genome (e.g. Myotis lucifugus)
wget ftp://ftp.ensembl.org/pub/release-84/fasta/myotis_lucifugus/dna/Myotis_lucifugus.Myoluc2.0.dna.toplevel.fa.gz
gunzip Myotis_lucifugus.Myoluc2.0.dna.toplevel.fa.gz

#List of all the possible fragments produced by the association of SbfI and SphI
./ddRAD_enzyme.pl -i Myotis_lucifugus.Myoluc2.0.dna.toplevel.fa -2 SbfI -1 SphI > cuts.SbfI_SphI.txt

#List of all the possible fragments available for a ddRAD - (SbfI------SphI)
./ddRAD_enzyme.pl -i Myotis_lucifugus.Myoluc2.0.dna.toplevel.fa -2 SbfI -1 SphI -rad > rad.SbfI_SphI.txt

• find_pattern.pl: Test for diagnostic alleles or patterns between populations using raw STACKS RAD outputs

#extented help (PLEASE READ IT)
./find_pattern.pl

#Simple test
./find_pattern.pl --haplotypes batch_1.haplotypes.tsv --population pop.txt -v --group 2 -d

• needle_matrix.pl: use EMBOSS/needle aligner to perform all pairwise comparison and report similarity or identity values.

#extented help (PLEASE READ IT)
./needle_matrix.pl

#Simple test
./needle_matrix.pl --in sequences_AA.fa --db sequences_AA.fa -s >results.tsv

Issues

If you have any problems with or questions about the scripts, please contact us through a GitHub issue.

Contributing

You are invited to contribute new features, fixes, or updates, large or small; we are always thrilled to receive pull requests, and do our best to process them as fast as we can.

License and distribution

This code is distributed under the GNU GPL license v3. The documentation, raw data and work are licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.​