I am trying to map paired end reads to contigs I have assembled from a metagenome. I would like to keep all alignments up to some edit/hamming distance threshold, so I thought yara (formerly masai) would be good for this task. Unfortunately, when I try to index my contigs, I get the error message "Maximum number of contigs exceeded."
Also, the reads I am mapping were trimmed to remove Illumina adapters and thus vary in size within each mate file from the paired ends. I formerly checked out mrsFast and saw it can't handle this type of data. Has anyone else bumped up against this case that can recommend a tool to get the job done?
With much appreciation, Roye