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7 hours ago by

I have a large number of episomes (don't know what they all are and some might be present with human sequence) that I would like to align against along with the human genome. Is there a way to somehow merge BAM files so I can save time from building BWA indices each time for the genome + episome? How do people currently address the problem of having large eukaryotic genomes with multiple small additions/changes (genome + multiple different plasmids)?

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