chloroExtractor: extraction and assembly of the chloroplast genome from whole genome shotgun data

The chloroExtractor is a perl based program which provides a pipeline for DNA extraction of chloroplast DNA from whole genome plant data. Too huge amounts of chloroplast DNA can cast problems for the assembly of whole genome data. One solution for this problem can be a core extraction before sequencing, but this can be expensive. The chloroExtractor takes whole genome data and extracts the chloroplast DNA, so different DNA is separated easily by the chloroExractor. Furthermore, the chloroExtractor takes the chloroplast DNA and tries to assemble it. This is possible because of the preserved nature of the chloroplasts primary and secondary structure. Through k-mer filtering the k-mers which contain the chloroplast sequences get extracted and can then be used to assemble the chloroplast on a guided assembly with several other chloroplasts.

Freely available at GitHub:  https://github.com/chloroExtractorTeam/chloroExtractor

Publication: http://joss.theoj.org/papers/eaceb6ac6723a3ea5749f7f50d4a4ad4