PALMapper, a fast and easy-to-use tool that is designed to accurately compute both unspliced and spliced alignments for millions of RNA-Seq reads. It combines the efficient read mapper GenomeMapper with the spliced aligner QPALMA, which exploits read-quality information and predictions of splice sites to improve the alignment accuracy.
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Jean, G., Kahles, A., Sreedharan, V.T., De Bona, F., Raetsch, G.,
RNA-Seq Read Alignments with PALMapper,
Curr. Protoc. Bioinform., 32:11.6.1-11.6.38, 2010.