I'm using SPAdes to assemble bacterial genome sequenced on illumina platforms.
I have a few files that I'm struggling to assemble due to the incredibly large coverage of my raw reads. Anything over 250x seems to cause spurious assemblies, with the final fasta being three times the expected size.
At first I thought it could be contamination, but annotation shows only target species genes present. I've heard SPAdes can struggle with particularly high coverage files - so what can I do to get them assembled? One file is ~500x coverage...