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Log Racon polish edits #69
Description
Hi, I am following the polishing method of Mc Cartney et al., 2022, where Racon's liftover and master branches were used. However, I have no idea of how to use this two and would like to ask.
The detailed method is as follows:
The filtered alignments produced are then used as input to Racon, here the Racon liftover branch is utilised. This is an extension of the master branch of Racon with two custom features:
- BED selection of regions for polishing
- logging the changes introduced to the draft sequences to produce the polished output (in VCF, PAF or optionally SAM format)
Racon is run with default options except for two new logging options -L out_prefix and -S, which store the liftover information between the input and output sequences.
Activity
rvaser commentedon Jul 13, 2022
Hello,
could you please provide the DOI of the paper in question? @isovic implemented the liftover branch so he might know more.
Best regards,
Robert
justdx commentedon Jul 13, 2022
Sorry for the poor consideration, and here is the DOI https://doi.org/10.1038/s41592-022-01440-3. Thanks.
yeeus commentedon May 31, 2023
hello, I'm also following the polishing method of Mc Cartney et al., 2022, but I couldn't find the right version. Can you please tell me that have you solved this problem? Best wishes!
justdx commentedon May 31, 2023
unfortunately, it hasn't been resolved and I didn't run this step