Advice for reconstructing plasmids

[iaposto]

Congrats for your work! I would be grateful for any advice on how to use the output of RFPlasmid to reconstruct the different plasmids that might be present in an assembly by e.g. attempting to bin predicted plasmid contigs into discrete units. I was also wondering if you have any plans to integrate such an approach in your tool.

Thanks!

[Aldert Zomer]

I think this tool might help: https://academic.oup.com/bioinformatics/article/36/12/3874/5818483 . The output of rfplasmid can be used as input for gplas if I'm not mistaken (you need to make a few changes).

[iaposto]

I tried gplas before using some closed E. coli genomes of our lab for benchmarking but results were not satisfactory (mixed plasmids in same bin, at least for my dataset). The input for gplas is gfa (assembly graphs) but I will check if it's possible to tweak it in order to accept fasta and try it.

[Aldert Zomer]

You can ask Anita Schurch, i believe she was working on making it compatible. Op do 18 mrt. 2021 17:54 schreef feanor1914 ***@***.***>:

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I tried gplas before using some closed E. coli genomes of our lab for benchmarking but results were not satisfactory (mixed plasmids in same bin, at least for my dataset). The input for gplas is gfa (assembly graphs) but I will check if it's possible to tweak it in order to accept fasta and try it. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#15 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACPJGW3A2RIVHOVUEMG344TTEIV3JANCNFSM4ZMN76WA> .

[iaposto]

Will do, thanks.