Hello guys,
After I played around with Mosaik aligner for a while, I started to wonder a question: how to evaluate the quality of assembly after increase mismatch number. Since mosaik does not have a limitation for mismatches in the reads mapping to the reference, I found that if I increases the mismatch, my consensus always get longer, and number of reads mapped always get increased (which also make sense). But how do I know it is not achieved the improvement by jeopardise the assembly quality, such as mapping a lot of reads into wrong position. Is there any way to evaluate the assembly quality?
Thanks!
After I played around with Mosaik aligner for a while, I started to wonder a question: how to evaluate the quality of assembly after increase mismatch number. Since mosaik does not have a limitation for mismatches in the reads mapping to the reference, I found that if I increases the mismatch, my consensus always get longer, and number of reads mapped always get increased (which also make sense). But how do I know it is not achieved the improvement by jeopardise the assembly quality, such as mapping a lot of reads into wrong position. Is there any way to evaluate the assembly quality?
Thanks!
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