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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
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contigs numbers were reduced #98

Closed njaupan closed 5 years ago

njaupan commented 5 years ago

Hi,

I ran Racon on a Canu-assembled 130X plant genome. It reduced from original 530 contigs to 510 by first round Racon and to 507 contigs by second round Racon. It is weried as Racon should not change contigs number if i understand correctly. I re-run Racon three times, it didn't help. Here is the script, can you tell me why?

~/minimap2-2.12_x64-linux/minimap2 -t 12 --MD -ax map-ont canu.fa reads.fa > 1.sam ~/racon/build/bin/racon -t 12 -w 1500 reads.fa 1.sam canu.fa > racon1.fa

Best, panpan

rvaser commented 5 years ago

Hello, racon by default does not return sequences which were not polished, hence the decrease in contig number. You can retain them with the -u (--include-unpolished) option.

Best regards, Robert

njaupan commented 5 years ago

I see, Thank you!