I read the paper Reducing assembly complexity of microbial genomes with single-molecule sequencing, and I find it use PacbioToCA to do self-correction. But I think PacbioToCA uses short reads(NGS reads) to do hybrid read correction, not self. And the paper says it uses PBcR and NGS reads to do hybrid read correction, and in the section PBcR correction pipeline in that paper, it mentioned it's feasible to use C2 reads to do self correction. I'm confused what method it really use to do self correction.
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http://canu.readthedocs.io/en/stable/ Is the latest implementation of a pipeline to assemble Pacbio only data based on Celera Assembler (CA). -
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First it uses short reads, If there is no short reads it uses long reads, now as rhall mentioned it uses long reads only in a new software called canuComment
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