I have recently assembled my shotgun metagenomic reads using metaSPADES without changing any default settings. I then upload them to MG-RAST for annotation. However, some of the samples have contigs greater than the maximum length cut off (500,000bp). According to the manual, the MG-RAST pipeline has a hard time annotating reads/contigs that contain multiple organisms. If I reduce my K-mer size, would this result in shorter contigs? Or does anyone have any other suggestions for adjusting contig length without manually separating them and compromising coverage statistics?