I’m looking for a short read mapper to map metagenomics samples against wide range of microbial genomes.
I just need to know the best mapping so aligner that optimized to find variants is unnecessary.
I know that it is common to use Bowtie2 and BWA but wondering whether you have further recommendations.
The main need is a fast aligner that would find the best hit for each pairs of reads.
I did not found any good benchmarking for that purpose.
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