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.
Short-read aligners are not designed to distinguish between closely related species. Results that you get with those could be highly misleading as equally well-aligned reads would be assigned in a random fashion to one of the contigs.
Thus if two species share a long region then even if you have only one of the species present a short read mapper might indicate that both are there at 50% abundance.
If the goal is to evaluate the abundance of various species then use a dedicated tool that has a built-in mechanism to account for similarities between species.
Kraken2 is kmer based, not a read aligner.
True, Kraken2 is kmer-based. Is there a reason to prefer KrakenUniq over Kraken2? Kraken2 is a follow-up to KrakenUniq; is faster and has a lower memory footprint; and has comparable accuracy, sensitivity, and positive predictive value (see Fig. 2).
Results on mock communities, less false positives. I'm not a great believer in the accuracy statistics of tool authors, they are invariably a little better than the rest. Trust the independents, the systematic comparisons, and your own results on "known" mocks.