The pyrocleaner is intended to clean the reads included in the sff file in order to ease the assembly process. It enables filtering sequences on different criteria such as length, complexity, number of undetermined bases which has been proven to correlate with poor quality and multiple copy reads. It also enables to clean paired-ends sff files and generates on one side a sff with the validated paired-ends and on the other the sequences which can be used as shotgun reads.
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Mariette J, Noirot C, Klopp C.
Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool.
BMC Research Notes 2011, 4:149