Hello, I am trying to sequence pichia genome with a transgene insertion. I have paired end reads from Illumina miniseq.
I tried using BWA with wild type genome as reference followed by samtools mpileup and vcfutils to get a consensus sequence. However, in that approach, my insertion vector was not a part of the final assembly. I aligned the reads against the my vector sequence and saw over 40,000 reads aligning to the vector sequence so I am sure that my insertion vector is present in the genome.
I then used Abyss to do a denovo assembly and used the scaffolds generated from abyss to align against the wild type genome and again I ended up with a final assembly with no vector sequence.
Is there a way to get a final assembly with four chromosomes (Pichia pastoris) and my vector sequences present?