I want to use MEGAN on NexSeq 2x150 reads that I have assembled (R1 and R2 files trimmed and assembled together), thus obtaining longer reads. I’ve read that Diamond is not recommended for long reads. Actually, I’ve already employed Diamond on my datasets and only a low proportion of reads are assigned. My question is whether MALT could be used on long reads. I’ve read that LAST is also recommended for long reads.
Looking forward to a reply. Thanks in advance.