search

ablab / quast

Genome assembly evaluation tool
http://quast.sf.net
Other
395 stars 76 forks source link

download icarus consensus sequence #150

Open marctormo opened 4 years ago

marctormo commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

Thanks for your comment.

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