lotteanna/Bioinformatics

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.

- GBS1a_ref_genome.md: how to get started with your (possibly highly fragmented) reference genome
- GBS1b_Stacks_notcomplete.md: 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_LFMM
- GBS_Stacks: de novo assembly of paired end GBS reads