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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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What does the no-trimming flag do? #168

Closed zacksaud closed 3 years ago

zacksaud commented 3 years ago

Hi,

Firstly, many thanks for this excellent piece of software. My question concerns the no-trimming feature. What exactly does this do? Does it not trim the end of reads to fit the assembly? Or does it not trim the extreme ends of contigs if there is very low coverage there?

Many thanks in advance

Best

Zack

rvaser commented 3 years ago

Hello Zack, the --no-trimming option disables consensus trimming in each window. Racon creates partial order graphs within non-overlapping windows of each contig, and the consensus calling algorithm can have low coverage ends. Therefore we trim away bases from each consensus sequence until the base coverage reaches half the coverage of the corresponding window.

Best regards, Robert

zacksaud commented 3 years ago

Dear Robert,

Many thanks for this information.

Best Zack