2bRAD-denovo

Download the latest updates from https://github.com/z0on/2bRAD_denovo



2bRAD is a method for cost-efficient whole-genome genotyping, described in Wang et al 2012
http://www.nature.com/nmeth/journal/v9/n8/abs/nmeth.2023.html

This project is about analyzing 2bRAD data without a genome reference.

Scripts and walkthroughs for:
- trimming and quality filtering;
- removing PCR duplicates;
- assembling loci;
- calling variants (SNP-wise and haplotype-wise);
- recalibrating quality scores based on genotyping replicates;
- smart-thinning and final filtering;
- quality assessment based on replicates.

Also included are walkthroughs for analysis:
- computing Weir and Cockerham Fst
- BayeScan
- ADMIXTURE
- fastSTRUCTURE