I want to screen some aligners to pick the most sensitive one.
What are the good aligners that work with Illumina hiseq paired end data? My genome is about 390 MB.I have 100 crore reads (paired end 502 crores). Is it a good idea to pick up about 2100 reads and first do a BLAST search to identify their position, and then align those with each aligner?? I know that 200 reads are very few to assess the performance of an aligner. But, since I also have to manually check each of them by BLAST, I'm thinking of the minimum.
Also, looking for leads to shortlist some good aligners.