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 pour 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.
- pyrocleaner_galaxy_tool_V1.3.tar.gz for pyrocleaner version 1.3 - provides all files to run the pyrocleaner within the galaxy workflow manager. Also available from the Galaxy Tool Shed.
- pyrocleaner_ergatis_component_V1.3.tar.gz for pyrocleaner version 1.3 - provides all files to run the pyrocleaner within the ergatis workflow manager.
- pyrocleaner_V1.3.tar.gz - Use Seqio instead of Bio.SeqIO as input/outpout sequences library to spead up the process and delete the Biopython dependance.
- pyrocleaner v1.2 - Fix a bug when using --clean-pairends.
- pyrocleaner v1.1 - Add --aggressive option to keep only 1 read per cluster, add --clean-quality cleaning option to clean reads based on basepairs quality.
- pyrocleaner v1.0 - Here is the first packaged version of the tool.
How to cite
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.