Minipolish alternatives

I am trying to assemble a bacterial genome sequenced with long reads (miNION), with Minimap2/Miniasm. The assembly works fine (it produces 1 contig; the same as with Flye and Raven+Racon) but then I need to polish the assembly, and Minipolish is not in the Galaxy toolshed.
Does anyone have any suggestions to overcome the absence of Minipolish? I would like to feed the three assemblies to Trycycler/Medaka to get a more robust asembly, but it seems that polishing after Miniasm assembly is essential…

Hi @iker,
currently, the best alternative would be to use Racon. I’ll work in order to include minipolish for the next week.

Regards

Thanks very much for including Minipolish. It will allow us to complete the Minimap2/Miniasm/Minipolish workflow…
About Racon… That is what I thought in the beginning and I tried it. There must be something I am doing wrong because I always get an error… I transform the GFA into fasta (using the tool GFA to Fasta). Then I feed Racon with the three files: the raw reads (I’ve tried fastq and fastqsanger), the overlaps (I’ve tried the PAF file obtained with Minimap2 and a SAM created from the BAM obtained with Minimap2 too (-O BAM), and the draft assembly (in fasta). I always get an error: empty overlap set! But the overlap file is not empty… Any clues why? I attach a screenshot of the look of the PAF file as seen in Galaxy


Thanks very much again,

iker

Hi @iker,
could you share your Galaxy history with me? Also, minipolish will be available from Monday.

Regards

Done!
Thanks very much again!

Hi @iker,
as I mentioned to you in the email, the problem is that, in order to generate the overlap file, the reads should be mapped against the reference genome.

Regards

Aha! Thanks very much for your help!!