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Unicycler has now made a huge release to v0.5.0. So, it would be nice to have the pipeline now using this version.
For that, a few fixes in the pipeline's environment and scripts should be done would be required:
Unicycler now accepts the newest SPAdes version thus the v3.13 binaries would no be necessary anymore
Unycler now do not correct reads prior to assembly, thus, the information about --no_correct should be remove
Unicycler now do not polishes the assembly in the end, thus, a new step for pilon polish is required after it's assembly
This already happens for hybrid assemblies, however, should also be performed for Illumina assemblies.
Unicycler has now descontinued it's script unicycler_polish which was used inside the MpGAP's pilon polish module for paired end reads
Thus, this module needs to be updated to do not use this script and perform only a single polishing with pilon either with single (which is already this way) or paired end reads.
This, removes the dependency on ALE binaries
Obs: For now, this release will not impact the pipeline since it is stick to the v0.4.8. However, for using the new one, these observations should be addressed.
The text was updated successfully, but these errors were encountered:
Unicycler has now made a huge release to v0.5.0. So, it would be nice to have the pipeline now using this version.
For that, a few fixes in the pipeline's environment and scripts should be done would be required:
--no_correct
should be removeunicycler_polish
which was used inside the MpGAP's pilon polish module for paired end readsALE
binariesObs: For now, this release will not impact the pipeline since it is stick to the
v0.4.8
. However, for using the new one, these observations should be addressed.The text was updated successfully, but these errors were encountered: