download icarus consensus sequence

[marctormo]

Hi there!

I was wondering if there's any chance to download a consensus sequence from icarus viewer. I made a de-novo assembly, and I'm running quast with a reference file. Maybe there's a way to download a consensus of the contigs/scaffolds sorted as the alignment from icarus viewer (and with the predicted genes with the new "reference" coordinates).

Thanks for your support!

[alexeigurevich]

Hi! Could you please clarify your desired output? Do you expect to get fragments of the reference that correspond to the aligned parts of your assembly (i.e. remove reference parts not covered by the assembly)? Or do you want to extract the aligned parts of your assembly (i.e. remove unaligned parts from the assembly)? Both genomic sequences will be similar but may have a per-base difference due to real SNPs or single nucleotide errors in the assembly.

[marctormo]

Thanks for your comment.

I was looking for the first option, to get the fragment's consensus from my assembly.