isovic
option setting a list of scaffolds to correct
Hi,
Other software packages such as pilon or samtools include an option to limit the processing on a set of scaffolds. The user provides a text file with one scaffold name per line and the correction process is limited to this list. This enables to run several corrections in parallel with the same input files but on different scaffolds. Could you add this option to racon?
Hello, what would be the use case of this option except maybe running on clusters? I do not fancy the idea of parsing nonstandard formats especially when a simple preprocessing script could just split the file into several smaller ones.
Best regards, Robert
Hi,
Thank you for you answer.
If you do not want to parse non standard file formats, the option could be to use a parameter string 'scaffold1:start1-end1,scaffold2:start2-end2,..,'
The other use case I see is when you only want part of the result, for example a given scaffold or some scaffolds, why would you polish all to get those ones.
Kind regards,
Christophe KLOPP MIAT INRA Toulouse CS 52627 31326 Castanet-Tolosan Tel: 33 5 61 28 50 36 Email: [email protected] @ChristopheKlopp http://www.sigenae.org/ http://bioinfo.genotoul.fr/
De : Robert Vaser [email protected] Envoyé : mercredi 2 mai 2018 19:51 À : isovic/racon Cc : Christophe Klopp; Author Objet : Re: [isovic/racon] option setting a list of scaffolds to correct (#70)
Hello, what would be the use case of this option except maybe running on clusters? I do not fancy the idea of parsing nonstandard formats especially when a simple preprocessing script could just split the file into several smaller ones.
Best regards, Robert
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I still think that a preprocessing script is a better option. I'll think about it a bit more.
Best regards, Robert