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Traditional quantification algorithms that use alignments of sequencing reads to the genome or transcriptome require substantial computational resources (Teng et al., 2016) and do not scale well with the rate at which data are produced (Kodama et al., 2012). Sailfish (Patro et al., 2014) achieved an order-of-magnitude improvement in speed by replacing traditional read alignment with the allocation of exact k-mers to transcripts. Kallisto (Bray et al., 2016) achieves similar speed improvements and further reduces the gap in accuracy with traditional alignment based methods by replacing the k-mer-counting approach with a procedure called pseudoalignment, which is capable of rapidly determining the set of transcripts that are compatible with a given sequenced fragment.
(Teng et al., 2016) A benchmark for RNA-seq quantification pipelines. Genome Biology.
(Kodama et al., 2012) The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Research.
(Patro et al., 2014) Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nature Biotechnology.
(Bray et al., 2016) Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology.
(Patro et al., 2017) Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods.