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1. Trimming, adapter-removal, and size filtering (BBDuk, http https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/)
1.1. Use bbduk.sh to remove the adapter sequence from the 3' end of the reads and trim homopolymers.
1.2. Split up the reads into short read and long read fractions.
1.3. Short reads read into the adapter sequence AND are shorter than 31 bp and are processed for miRNA alignment.
1.4. Long reads are kept separate for alignment to the reference genome.
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Alternative programs for read mapping can also be used. A comparison of some alignment programs for small RNA-Seq data can be found in Tam et al., 2015.
Example: Small RNA analysis pipeline built using modified Nextflow workflow tool: https://nf-co.re/smrnaseq/1.0.0 .