I want to use MEGAN for my microbiome study. I have illumina reads, which I have assembled into contigs. I want to run MEGAN on my reads/contigs.
I am sort of unsure what should I use. I can run MEGAN6 on my small illumina reads or MEGAN-LR on my assembled contigs. Which is the better option for me?
I have read that the MEGAN-LR is specifically written for long reads produced from PacBio and other technologies. However, my assembled contigs are in the range of 300nt-286,000 nt. How sensitive MEGAN-LR would be on this long size range?