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Old 01-20-2014, 03:48 PM   #1
SDK
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Default Program to Randomly Chop Sequence files?

Hey Guys,

First post! Anyone know of a program one could use to chop up a sequence file (15kbp; mtDNA genome) into random smaller fragments (~150bp)? I want to chop up the sequences of 5 or 10 species, mix them together and then see if alignment software can tease them apart to the correct species. It's a test for some NGS we are planning to run.

Thanks for any input!!
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Old 01-20-2014, 04:02 PM   #2
GenoMax
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Assuming that you want to simulate NGS reads (and not just FASTA fragments, though you could convert the simulated fastq to fasta later) ART: http://www.niehs.nih.gov/research/re...tatistics/art/ is an option.

Here is a past thread on this that has other suggestions: http://seqanswers.com/forums/showthread.php?t=9961
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