Scripts for transforming GBS data to analyses
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Type Name Latest commit message Commit time
Failed to load latest commit information.


Yup, this all might seem super simple. Unfortunately, not all of us are hardcore computer programmers and have to learn some stuff from scratch. Here I aim to give a guide how to do some basic and more hardcore bioinformatics from fasta to population genetics and landscape genomics. Not finished yet, so stick with me for more updates and troubleshooting.

- how to get started with your (possibly highly fragmented) reference genome
- Darn, no reference genome available. We can also build one *de novo*
- GBS2_raw2filtered: raw paired end GBS reads to alignment ready files;
- GBS3_bwa: Align filtered paired end GBS reads with fragmented reference genome
- GBS4_gatk: Indel realignment, Calling SNPs and Genotypes using UG and HaplotypeCaller
- GBS5_vcffilter: filtering vcf files with custom perl scripts
- GBS6_STRUCTURE: transforming custom SNP and genotype tables to STRUCTURE and running the program
- GBS_BayEnv
- GBS_Stacks: de novo assembly of paired end GBS reads