scaffolding with output from other assemblers?

jts / sga

de novo sequence assembler using string graphs

http://genome.cshlp.org/content/22/3/549

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scaffolding with output from other assemblers? #78

Closed bcthomas closed 10 years ago

bcthomas commented 10 years ago

Is it possible to use the sga scaffolder with the contigs output from other assemblers?

jts commented 10 years ago

Yes it is and the workflow is very similar to scaffolding contigs generated by SGA. Some information can be found here (see the note on "If you are scaffolding contigs not produced by sga assemble"):

https://github.com/jts/sga/wiki/Scaffolding-multiple-libraries

Feel free to ask questions on the sga-users mailing list if you need help.