RAD・MIGtools

This is a collection of scripts for processing and analysing genome-wide sequencing data.

I mainly focus on dealing with Reduced Representation Sequence (RRS) data obtained by RAD-seq, MIG-seq and GRAS-Di is assumed (but any other data could be applied).

Contents

• Calculate sequence dissimilarity
• Calculate and plot 1d SFS from VCF files
• Admixture

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Calculate sequence dissimilarity

calc_pairwise_sim.R is the script which reads phylip format generated by Stacks to calculate number of substitutions. You can visualize heat maps as well.

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Calculate and plot 1d SFS from VCF files

Calculate SFS

# code block
Rscript xx.R xx.vcf

Plot SFS

Rscript xx.R xx.vcf

Plot SFS with geometric distribution

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Admixture

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License