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markhilt / ARBitR

ARBitR: Assembly Refinement with Barcode-identity-tagged Reads
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Scaffolding supernova 10x #5

Closed shabirmoosa closed 3 years ago

shabirmoosa commented 3 years ago

hi,

Could you provide more info on how I can scaffold the fasta files generated using supernova assembly ?

markhilt commented 3 years ago

Hi! The principle is the same as for any assembly: Map the linked reads with the mapper of your choice (though make sure the barcode is given in the BX tag) and provide the fasta and bam files to ARBitR.

Supernova can create different fasta files depending on your needs. If you're using ARBitR I'm guessing you want the "pseudohap" format from supernova.