ChloroExtractor: A fully automated plastid assembly pipeline reveals dozens of novel plastid genomes

In times of large scale high troughput sequencing, novel plastid genomes mostly emerge from host genome sequencing projects. Here we present ChloroExtractor, a fully automated pipeline designed to generate high quality plastid assemblies from heterogeneous short read data. By applying our software to 100 publicly available plant sequencing libraries, we salvaged 27 novel and complete plastid genomes across a wide range of plant taxa. Thus, we consider ChloroExtractor a valuable tool in the process of further unraveling plastid biology and evolution