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HINGE for minimap #112
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Hi @ebioman , HINGE (tentatively) supports minimap, instead of passing |
Hi @fxia22 |
@ebioman We have our own filtering which contains scrubbing(mainly based on coverage). BTW, the minimap pipeline has not draft assembly and consensus module, so the assembly graph will be final output. |
Hello @fxia22 |
Hi
Update: the strange thing is that if I remove all options and just execute If I do the same with DALIGNER it succeeds:
I used minimap 0.2-r124-dirty |
Sorry to push this, but any ideas what might be wrong - is it working for you in the latest version? |
We have fixed the bug and you can run the pipeline before There seems to be a nice work around using minimap2. The pipeline for the lambda-virus would be the following:
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Thank you very much, I will give it a try today. Update: If I try the original --fasta and --paf combination I still encounter a problem
Is there anything in the config which has to be changed or am I missing something obvious ? I looked at the work-around but the step of recalculating the cigars is unfortunately very time-consuming and beats the idea of replacing DALIGNER by minimap2 in order to gain speed in assembly. |
Sorry did not see the update to the comment (It looks like we don't get notified about it). The way we seem to be handling this is to convert the |
Minimap2 has also If it is still valid after this step
Thank you in advance. |
Hello
I found that intriguing sentence in your paper
"Therefore, integrating HINGE with other overlapping tools such as MHAP or Minimap can be done if different levels of alignment sensitivity or memory usage are required"
Is this a theoretical possibility, something you already started to look into or even possible with current code?
Cheers
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