Is it possible to run falcon_unzip on HGAP4 output from SMRTlink ?

PacificBiosciences / FALCON_unzip

Making diploid assembly becomes common practice for genomic study

BSD 3-Clause Clear License

30 stars 18 forks source link

Is it possible to run falcon_unzip on HGAP4 output from SMRTlink ? #161

Closed Philosamia closed 4 years ago

Philosamia commented 4 years ago

Hi, I just finished assembling my genome on SMRTlink GUI v8. Is it possible to run Falcon_unzip command line on HGAP4 output from SMRTlink GUI, or do I have to re-run falcon on command-line and then run unzip?

Thanks

pb-cdunn commented 4 years ago

You can try python3 -m falcon_kit.mains.hgap4_adapt --help. In theory, that can create symlinks to make a smrtlink run look like a falcon run, so falcon_unzip can then be used.

Unfortunately, smrtlink directory names may have changed, and we have not been keeping the adapter up-to-date. But it might work for you.