Standardizing the cpDNA assemblies makes it easier to run many downstream analyses, especially plastome comparisons. This simple script is written to standardize any cpDNA assembly to start from an LSC region followed by IRa, SSC, and IRb regions.

Install the below software and add them to the environment

samtools (tested with v1.13)

blast+ (tested with v2.12.0+)

git clone https://github.com/SaiReddy-A/Standardize_cpDNA.git

./standardize_cpDNA.sh -i input.fa

The output is a standardized fasta file written to input.standardized.fa

./standardize_cpDNA.sh -i test.fa

Any suggessions and comments are greatly appreciated!!