NGSGenotype

Analysis pipeline for genotyping individuals based on either microsatellites or SNPs (Single Nucleotide Polymorphisms).

Usage

Clone down this repository and move into it:

git clone https://github.com/CGI-NRM/NGSGenotype
cd NGSGenotype/

Move your data into the Raw_data-folder:

mv [folder with your data in it]/*.fastq.gz ./Raw_data/

If you have paired end data, merge reads with (log will be saved to 'bbmerge_log.out'):

cd Merged_data/
bash merge_all_pairs.sh

Trim all primers, choose primer file as well as if data was merged of single end (log will be saved to 'cutadapt_log.out'):

cd ..
bash cutadapt_script.sh merged Primers/Bear_SNP_all_loci.fa # for merged data with bear primers

# or:
bash cutadapt_script.sh single Primers/L_vulgaris.fa # for single end data with Lissotriton primers

Microsatellites

Continue analysis in R using the rmarkdown file 'ngsgenotype.rmd'.

Single Nucleotide Polymorphisms

Trim the superflous sequences around the SNPs:

bash filter_out_SNPs.sh # currently hardcoded for bear SNPs

Genotype the SNPs:

cd Genotyped_SNPs/
python snpotypewriter.py ../Filtered_data/SNP_filtered/ > genotyped_SNP_data.csv

# or, if data is divided into chunks (where chunk folder names start with "chunk_"):
bash loop_over_chunks.sh ../path/to/folder/with/chunks/

And then continue analysis in R using the rmarkdown file 'ngsgenotype_snp.rmd'.