Aligners

Traditional sequence alignment tools like BLAST are not well suited for next generation sequencing where one needs to align millions of short sequences very quickly. This has given rise to the development of a new class of short read aligners of which there are now dozens available. For small RNA-seq data alignment present certain specific challenges but standard aligners used for normal RNA-seq are usually adequate with the right parameters. The aligner and parameters will have an effect on the results, so trying more than one might be a good idea.

Currently smallrnaseq integrates bowtie (version 1) and subread. Though others can be added on request. These are free and easy to install on linux and OSX systems. On Ubuntu the command apt install bowtie subread installs both.

Links

http://subread.sourceforge.net/

http://bowtie-bio.sourceforge.net/index.shtml