Robert Vaser comments

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                                            Robert Vaser

[racon::Polisher::initialize] error: duplicate sequence <file_name> with unequal data

Are you trying to polish contigs or correct reads with each other? Please provide me with your command and descriptions of input parameters.

[racon::Polisher::initialize] error: duplicate sequence <file_name> with unequal data

I have trouble understanding your description. What is in the file?

[racon::Polisher::initialize] error: duplicate sequence <file_name> with unequal data

What do you need the reference genome for?

[racon::Polisher::initialize] error: duplicate sequence <file_name> with unequal data

Lets start from the beginning. You have some ONT data, is it DNA or RNA? Are you trying to assemble the sequenced genome or just increase the read accuracy?

[racon::Polisher::initialize] error: duplicate sequence <file_name> with unequal data

If you want to polish your reads with racon you should run the following: ```bash minimap2 -ax ava-ont --dual=yes > alignments.sam racon -f alignments.sam > polished_reads.fasta ``` If you want...

[racon::Polisher::initialize] error: duplicate sequence <file_name> with unequal data

I have been only using dnadiff from the Mummer package.

[racon::Polisher::initialize] error: duplicate sequence <file_name> with unequal data

I am running `dnadiff ` which creates several files. In *.report file is the summary of the comparison.

[racon::Polisher::initialize] error: duplicate sequence <file_name> with unequal data

Both files need to be in fasta format. Thank you for your kind words :)

[racon::Polisher::initialize] error: duplicate sequence <file_name> with unequal data

I have been using this one: https://github.com/marbl/MUMmer3. Did not yet try v4. You can download it with `git clone https://github.com/marbl/MUMmer3` and run `make` in the created directory.

[racon::Polisher::initialize] error: duplicate sequence <file_name> with unequal data

Hi Robert, the problem is that you have a sequence in `trimmed.fastq` and `reference.fa` that share a name. Try renaming your reference reads, rerun the minimap2 command and run racon...