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mikolmogorov / Ragout

Chromosome-level scaffolding using multiple references
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Multiple Assemblers #43

Closed kokyriakidis closed 5 years ago

kokyriakidis commented 5 years ago

Hello, could I use multiple assemblers like Masurca, Abyss etc, concat their contigs into one file and then use Ragout mapping this final file to the reference? Are there advantages to this approach? I am talking about de novo assembly with illumina reads only

mikolmogorov commented 5 years ago

Hi,

Ragout expects a single assembly without significant duplications as input - so the approach you have described will not work. What is your intuition of using a concatenate of multiple assemblies instead of selecting the best one and scaffold it using a reference? You can try to add other assemblies as extra draft references, but I doubt if will have any effect on the result, in case you have a good closely related reference.

Mikhail

mikolmogorov commented 5 years ago

Closed due to inactivity, feel free to reopen in case you have more questions.