I have performed de novo assembly for several metagenomic samples (using MegaHIT). The overall statistics (e.g. N50) seem OK. I am now interested in mapping the original reads to the contigs (to estimate coverage, which I need for binning).
However, it is not entirely clear what parameters should I use for the mapping, in terms of number of allowed indels, mismatches, longest indel etc. Are there any known practices? I was not able to find any.
Note: Olson et. al discuss the various sources of assembly errors, but I wasn't able to make it useful.