Can PlaScope work based on the assembly sequence from other soft?

[wanjinhu]

Hi there,
I am curious whether PlaScope can work based on sequences assembled by other software, such as soapdenovo, unicycler? Or just can work based on SPAdes ?

And also, can PlaScope work based on the assembled sequence of long-read sequencing(Pacbio, Nanopore)? The assembly sequence is from the software, just like canu, flye, unicycler and so on.

Thanks

[GuilhemRoyer]

Hi,

Currently Plascope can work only on SPAdes assemblies, but we plan to modify it. We prefer SPAdes assembly as we can get a deep coverage value from the header of each contig, but I agree that it will be interesting to enable other softwares.

For the Pacbio or Nanopore assembled sequences it cannot work for the same reason (we need a SPAdes-formated header in the fasta file).

Best

[jpaganini]

Hi Guilhem,

I had to use PlaScope coupled to some Unicycler assemblies. So, I've modified the code to include an assembler flag. Would you like me to do a pull request?

Thanks for developing this tool! It works like a charm!

Cheers,

[GuilhemRoyer]

Hi J.,

Thanks for modifying the code and having proposed a version adapted to another assembler. Sure it will be great if you can do a pull request.

Hope the tool will help in your work!

Guilhem

[duboism]

@jpaganini I have a few comments on the code (see the PR).

[duboism]

#4 has been merged. So I guess that the answer to this issue is "yes, at least with unicycler".