Hi all

I'm currently working on a de novo assembly in a region of the Capsella rubella genome, which has so far been quite unsuccessful.

I'm working on 150-bp paired end Illumina reads, and the individual is of the same genotype as the C.rubella reference.

The reads are mapped using bwa-mem. I have filtered my SAM files for mismatches, allowing up to 10% (15) due to the difficulty of mapping to repetitive regions. The alignments are then taken through picard SamToFastq and subsequently I trim the reads.

I have used SPAdes on these reads, and am able to reconstruct 19000/30000 bp for this region. Given that these reads come from the same genotype as the reference, I was expecting the mapping and assembly to be more straightforward.

Any suggestions would be most appreciated.