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  • De novo assembly strategy

    Hey all,
    I have been working with 98 million Illumina SE reads (RNA) and doing de novo assembly in CLC workbench. In my initial assembly I produced 170,000 contigs that I was able to identify using Blastx in Blast2GO. However, I have just received 40000 Sanger sequences from another researcher so I want to include these in the assembly to improve my 'transcriptome'. Does anyone have any advice on the optimal workflow for the assembly? Should I;

    1. Perform de novo assembly on the Illumina reads followed by a second assembly using the Illumina contigs and the Sanger reads.

    2. Perform one round of de novo assembly using the Illumina reads and Sanger reads?

    My goal is further improve the assembly using the STM pipeline (Optimization of de novo transcriptome assembly from next-generation sequencing data. 2010. Yann Surget-Groba and Juan I. Montoya-Burgos, Genome Research, 20: 1432-1440).

    Thanks!

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