Disagreement When Computing Contig Alignments With Different Tools.

Question

[HG]

Hi everybody I need a small suggestion : After assembly of one listeria genome with "Spades" i want to plot reference genome with my contig file. So i am using Mauve and Quast 2.3 to plot . Now i am getting in Quast its around cover 30% of genome and in mauve in visually i can see its above 90% and when i am doing Blast with this contig file its showing above 99% query cover with reference file. Can anybody suggest me something which will be my promising result.

[Istvan Albert]

I doubt that any two alignments would turn up as being so radically dissimilar, as 30% with one tool and 99% with another. The solution is probably you are either interpreting the results incorrectly or that the runs were performed on different data.