search

isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
257 stars 48 forks source link

Output record of fixes #228

Open christopher-holt opened 1 year ago

christopher-holt commented 1 year ago

Is there a way to output a record of fixes made by racon (similar to --changes in pilon)?

isovic commented 1 year ago

Hi @christopher-holt ,

You can try out the liftover branch. It has a couple of new useful features, some seem to be what you are looking for:

        -L, --liftover <string>
            default: ''
            optional prefix of the output liftover files which convert
            the draft sequence to the output consensus. PAF and VCF files
            are always written with this prefix, and SAM can optionally
            be written if the -S option is provided.
        -S, --liftover-sam
            Used only in combination with the -L option, this writes out
            a SAM formatted alignment of the polished sequences vs the draft.
        -B, --bed <str>
            default: ''
            path to a BED file with regions to polish

Important note: diffs reported by the liftover feature are not extracted directly from the POA graph, but are instead obtained from polished-to-draft sequence alignment, so there may be slight difference (but most likely insignificant).

Hope this helps, Best regards, Ivan.