I am attempting to assemble a novel insect genome using several assemblers (abyss, spades, minia...etc). I've preprocessed the raw paired-end fastq files following the Palumbi Lab's: Simple Fool's Guide, which uses tools in the fastqtoolkit like quality trimmer, duplicate counter...etc. I also have two read versions, from different lanes, which I preprocess similarly and then concatenate. However, after running abyss and spades I am getting errors that my files contain unequal amount of reads. I just downloaded BBMap and will try to preprocess using this, but would like some advice. Thanks
I think you you used for trimming tools that are not aware of paired reads, so I think after using BBMap or skewer then you will not face the problem