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Old 05-08-2014, 02:14 AM   #3
Jeremy
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Location: Pathum Thani, Thailand

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It might be more effective to exclude mitochondrial sequence after the assembly, the mitochondria and chloroplast tend to form separate contigs anyway. Unless your plant species is Arabidopsis, only using the arabidopsis mitochondria and chloroplast genomes as a reference will likely miss a lot of mitochondrial sequence. Plant mitochondria can be very diverse in sequence content and size.
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