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Old 05-02-2011, 12:25 AM   #6
Location: Oslo, Norway

Join Date: Nov 2008
Posts: 415


If you have an assembly running, you will notice that after the phase where newbler reads all the sequence file, there is the 454ReadStatus.txt file. This file can be used even if the assembly is not yet finished to get to the reads with the linker: these will be marked _left and _right. Saves you from having to do the mapping of the linker yourself...

About the assembly speed: have you tried using more cpus's (with the -cpu flag) and the -large option?
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