This folder contains the Python scripts that I create whilst working towards my Ph.D in Medical Entomology (Population genetics of the malaria mosquito vectors Anopheles gambiae and An. farauti).
The second step in my WGS processing pipeline. Automates the BWA shell script, which aligns reads to the reference genome to generate a SAM file.
Removes [unmapped scaffolds] and [mapped scaffolds with only one SNP] from the .map file to facilitate SNeP Ne analysis. SNeP errors out when it hits a 0 or has <2 SNPs to compare
Creates multiple alignments (.maf) containing selected mosquito seqs. aligned to Drosophila melanogaster dm6.chr assemblies (http://hgdownload.soe.ucsc.edu/goldenPath/dm6/multiz124way/maf/) for further evolutionary inference.
Maps scaffolds in a .vcf file to chromosomes in the .agp file
Creates a fastq file of every individual's reads from a pooled demultiplexed file. I wrote this script because NCBI required each individual to have its own raw sequence files.
The first step in my WGS processing pipeline. Automates the trimmomatic shell script, which trims Illumina sequencing and other adapters from the reads.