Entering edit mode
4 weeks ago
RCMC
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0
Good day,
I am practicing genome assembly in preparation to both in class and research,
I used a P. aeroginosa genome (Illumina and Nanopore using Flye, racon, and Pilon) from SRA to practice but when I assess the data in QUAST against reference genome (PAO1), there are lots of misassembles produced (See figure) The assembly 1 is my assembled genome and assembly 2 is a random sequence obtained from NCBI datasets. As you see both assemblies indicated lots of assembly (In fact, almost all). Is this a problem that I should be worried about? Since there are almost literature on draft genome
I also tried the SRA PAO1 gene and produced the same results (Not shown since I accidentally deleted it)
What does this mean? You should add some clarification about what the colors mean in plot above. Does red indicate mismatch with PAO1 genome or green?
Unless you used the raw data for the reference assembly when doing this practice there is always a chance that the strain you used could be different than the reference genome.
Good day Red means misassembled regions (mostly relocations and inversions) and green means correct assembly
long shot: can it be you have a reverse (-complemented) assembly compared to the reference genome? (so in practice all the red should be green and vice versa)?