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Alignment-free isoform quantification software tools | RNA sequencing data analysis

Alignment-free isoform quantification software tools | RNA sequencing data analysis Traditional quantification algorithms that use alignments of sequencing reads to the genome or transcriptome require substantial computational resources and do not scale well with the rate at which data are produced. Sailfish achieved an order-of-magnitude improvement in speed by replacing traditional read alignment with the allocation of exact k-mers to transcripts. Kallisto 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.
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