What happened to Tombo Re-squiggle

Question

[turcoa1]

Hi,

What ever happened to the Tombo resquiggle algorithm. Oxford Nanopore Technologies said that remora replaces the functionality of Tombo. Tombo doesnt have support anymore however all I want is the re-squiggle algorithm. What is the equivalent command in Remora (for the tombo command below) that does the same as this command in Tombo. All I want to do is re-squiggle my raw output but I am struggling doing this with remora.

tombo resquiggle path/to/fast5s/ genome.fasta --processes 4 --num-most-common-errors 5

[Ram]

Related thread: Processing Fast5 files from ONT for direct RNA

[Joseph]

Hi,

Does anybody has the answer to this? I also want to resquiggle my data with Remora but do not quite get which is the appropriate command to do so.

[Ram]

Please do not add answers unless you're answering the top level question. Instead, use Add Comment or Add Reply as appropriate. I've moved your post to the right location this time, please be more careful in the future.

Answer 1

[colindaven]

I'd ask nanopore in the remora repository directly since as you say Tombo is deprecated, but state clearly what you want to achieve, what data you have from which ONT chemistry, and why resquiggle-like functionality is important to you.