Butter: High-precision genomic alignment of small RNA-seq data

Eukaryotes produce large numbers of small non-coding RNAs that act as specificity determinants for various gene-regulatory complexes. These include microRNAs (miRNAs), endogenous short interfering RNAs (siRNAs), and Piwi-associated RNAs (piRNAs). These RNAs can be discovered, annotated, and quantified using small RNA-seq, a variant RNA-seq method based on highly parallel sequencing. Alignment to a reference genome is a critical step in analysis of small RNA-seq data. Because of their small size (20-30 nts depending on the organism and sub-type) and tendency to originate from multi-gene families or repetitive regions, reads that align equally well to more than one genomic location are very common. Typical methods to deal with multi-mapped small RNA-seq reads sacrifice either precision or sensitivity. The tool butter balances precision and sensitivity by placing multi-mapped reads using an iterative approach, where the decision between possible locations is dictated by the local densities of more confidently aligned reads. Butter displays superior performance relative to other small RNA-seq aligners. Treatment of multi-mapped small RNA-seq reads has substantial impacts on downstream analyses, including quantification of MIRNA paralogs, and discovery of endogenous siRNA loci. Butter is freely available under a GNU general public license.