Qpalma is a tool to align spliced reads. The Qpalma algorithm uses quality values and information of predicted splice sites for the assessment of alignment accuracy.
RNA-Seq
De Bona F, Ossowski S, Schneeberger K, Rätsch G "Optimal spliced alignments of short sequence reads." Bioinformatics 2008; 24(16):i174-80 https://doi.org/10.1093/bioinformatics/btn300
PMID: 18689821
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