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RNA-seq has rapidly become the de facto technique to measure gene expression.However, the time required for analysis has not kept up with the pace of datageneration. Here we introduce Sailfish, a novel computational method forquantifying the abundance of previously annotated RNA isoforms from RNA-seqdata. Sailfish entirely avoids mapping reads, which is a time-consuming step inall current methods. Sailfish provides quantification estimates much fasterthan existing approaches (typically 20-times faster) without loss of accuracy.

Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms