We know that many bacterial genomes have repeated regions / genes. This repeated region can be totally identical between copies over the course of the genome, or it can have some variation. How do genome assembly tools treat these regions?
I am experiencing a problem with a sample that I am still unable to resolve:
I know that my sample has at least two not completely identical copies of the ITS region (already provided by PCR + Sanger sequencing). Among them, the first 237 nucleotides are identical then there are 195 nucleotides that vary and, finally, another 135 identical nucleotides.
When trying to align the sequenced genome (Illumina paired-end sequencing) with the Spades tool, in one of the largest scaffolds there is the ITS region with an annotation “NNN” in the variable part. But a small scaffold (
I believe the best way to solve this is to sequence your target genome with two different approaches such as Pacbio and Illumina.
Pacbio generates long reads, which are usually longer than the repeated regions of bacterial genomes. This way, the assembler will not get "confused" about the location of a particular read.
On the other hand, the error rate of Illumina technology is much lower than Pacbio, so it is a good complement to assemble a genome of high quality.
