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Old 09-16-2014, 12:13 AM   #2
WhatsOEver
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Location: Germany

Join Date: Apr 2012
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On a first glance, the mitochondrium seems quite enormous in size with a really low GC-content.
I would therefore assume, that you have whole genome sequencing data and that you didn't filter your reads in any way, did you?
Can you tell from which organism this is?
Does "24GB of data" mean you have 2x12GB fastq read files or you have 24Gbp of sequence information?

The following paper on mitochondrial genome assembly from WGS might also be of interest for you:
http://nar.oxfordjournals.org/content/41/13/e129
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