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Old 06-30-2014, 11:50 AM   #2
Location: Prague, Czech Republic

Join Date: Nov 2010
Posts: 40

Use mira assembler and make sure you feed it with untrimmed Illumina reads (do not do quality trimming on your own). It will remove Illumina adapters on its own. Regarding 454 data ... I cannot recommend any good adapter removal tool for it, except the one I wrote.
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