Assembly of Illumina paired end reads using Celera Assembler

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On our way to a finished assembly, we need to preprocess our reads. We could have just put all the reads into Celera Assembler, and let it sort out the error correction, deduplication and removal of paired end contamination from the mate pair library, but we do it step by step to have more control and hopefully get a better result. Some of the native solutions in Celera Assembler might not work as easily/fast/good as wanted either (the removal of paired end contaminants is pretty slow for example).

We have a set of reads that have been error corrected using merTrim from Celera Assembler, and now we want to assemble the paired end libraries to get a preliminary assembly where we can map the mate pair library back to. The reads we are going to use was produced following the Error_correction_of_Illumina_reads_using_Celera_Assembler how-to.