To make the gapfilling and scaffolding more useful for downstream analysis, is there any standard protocol for assembly polishing? As most of gaps filled by PBJelly will cotain lots of errors (from Pacbio reads), they may affect lots of downstream analyses. In addition, is it better to use error corrected PacBio read to run PBJelly? Are there any parameters need to be adjusted if error corrected PacBio reads are used?
Thanks.
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There is no PBJelly recommended standard protocol for assembly polishing. This is up to the users. If you were to use error corrected reads, the default parameters are still generally acceptable.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
To make the gapfilling and scaffolding more useful for downstream analysis, is there any standard protocol for assembly polishing? As most of gaps filled by PBJelly will cotain lots of errors (from Pacbio reads), they may affect lots of downstream analyses. In addition, is it better to use error corrected PacBio read to run PBJelly? Are there any parameters need to be adjusted if error corrected PacBio reads are used?
Thanks.
There is no PBJelly recommended standard protocol for assembly polishing. This is up to the users. If you were to use error corrected reads, the default parameters are still generally acceptable.