What are people's preferred aligners for small RNA-seq data (e.g. 20-30nt stranded reads containing miRNAs, siRNAs, piRNAs) these days? I've been using bowtie (version 0.x or 1.x, NOT bowtie2) for some time now to align such data to reference genomes. I'm quite fond of it. But I've caught some flak from peer reviewers recently along the lines of "Why don't you use aligner x instead"? Indeed, why don't I? I'd like to crowd-source the question to BioStars.

The key features for a small RNA aligner as I see them are:

1. speed (fast, obviously)
2. memory usage (small, obviously)
3. simplicity in usage / commands
4. sam/bam output format

I'm not worried about adapter-trimming as that's an easy problem (in my opinion anyway) .. for the purposes of this forum assume the reads fed to the aligner are pre-trimmed to get of adapters.

In general my thinking has been to not worry about gapped alignments or even mismatches too much because a) the reads are really short .. mostly 20-24 nts, so there's not a ton of confidence if you can't find an perfect alignment or at worst an alignment with one mismatch , b) there is very little evidence that miRNAs and siRNAs in the organisms I work with (mostly plants) span splice sites, and c) Usually I'm working in 'SNP-free' environments (inbred plants).

Anyway, I'd love to hear people's thoughts and current favorite aligners for this application.