Set of scripts used to create mitochondrial genome for Eleusine indica(Poaceae) it also includes scripts used to create a series of heatmaps from SRAs downloaded from NCBI, scripts used in exon assembly, alignment and analysis, scripts used for validation which will include those used to get information for connection plot, depth, and vizualize the comparisons of sequenced genome features to putative mitochondrial contigs.
I have divided scripts up based on parts of the project they were used for, such as cleaning, heatmap, exon_assembly etc... Several of scripts are provided to show the manner in which work was done and back up copies of my work.