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marbl / canu

A single molecule sequence assembler for genomes large and small.
http://canu.readthedocs.io/
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which one should l use? #1972

Closed ld9866 closed 3 years ago

ld9866 commented 3 years ago

I assembled a genome using HICANU software, now which FASTA file should I use for the next HIC mount? ccs_asm.contigs.fasta ccs_asm.unassembled.fasta ccs_asm.unitigs.fasta

brianwalenz commented 3 years ago

Contigs. More details on the outputs of Canu are at https://canu.readthedocs.io/en/latest/tutorial.html#outputs.

Please check which version of Canu you used. I think you might be using version 2.0. Version 2.1.1 is the latest and contains numerous improvements for HiFi data.

skoren commented 3 years ago

You also probably want to run purge_dups as recommended here: https://canu.readthedocs.io/en/latest/faq.html#my-genome-size-and-assembly-size-are-different-help

ld9866 commented 3 years ago

thank you! l will change the version and try to handle it.