I'm looking around for some input from fellow SEQers. I'm experimenting with different aligners. I'm looking for an aligner that does a good job of correctly mapping reads from duplicated sequences, while at the same time is used fairly commonly. I am already looking into bwa, bowtie, and snap, but I would like to add one more to the list. Any suggestions? Would novoalign or stampy be good choices?
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Best Aligner for Duplicated Sequences
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