Repository of the Masters thesis project in computational biology titled: "In silico RAD-Seq as a possible tool for ancestry determination: an application in Helicobacter pylori"
- Simulation reads of the reference genome: simread_WholeGenome_wgsim.sh
- Restriction enzymes fragment generations for RAD-Seq and ddRAD-Seq simulations: ddRADseqTools_Hpylori_Frags.sh
- Form the Fragments .fasta files in step 2 to generate illumina simulations of Pared End (PE_ReadSim.sh) and Single End (SE_ReadSim.sh). To run this illumina simulations the script needs the java project SimpleReadsSim.zip.
- From the illumina .fastq files in step 3 reads are mapped to the reference genome of the PE and SE reads: runBWA_PE.sh and runBWA_SE.sh
- Finding SNPS form the .bam files in step 4. :MultipleVariantCall_NGSEP.sh To run correctly this script need the .bai files form step 4, even though they are not used explicity called in the script.
- Build distance matrix from the .vcf files in step 5 and calculate the Neighbor joining dendrograms: MatrixDistance-NJ.sh
- Run structure analysis with StrAuto pipeline (http://strauto.popgen.org) from STR file: runStrAuto.sh To run this file convert the vcf file in step 5 to str with software PGDSpider_2.1.1.5 (http://www.cmpg.unibe.ch/software/PGDSpider/)
- Plot structure analysis: structurePlot.m. To run this file use only the probability of each population (columns) of each sample (rows) once the best k has been chosen.