I'm trying to extract the chloroplast sequences from my reads, as Whole Genome Sequencing was used to produce them.
This paper: http://www.sciencedirect.com/science/article/pii/S2214540013000169 mentions that to do this, they BLASTed their reads against all of the known genomes in the same family. For me, this family would be Fabacaea.
Does anyone know of a quicker way to do this besides manually downloading every FASTA file containing Fabacaea chloroplast sequences from NCBI? Or of a better way to extract chloroplast sequences from my reads? I do know that chloroplast DNA should be more abundant than other DNA because it is more highly repeated than nuclear or mitochondrial DNA.
Info about reads: 300bp average, paired-end reads from Illumina MiSeq
Thanks in advance!