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MapSplice is an algorithm for mapping RNA-seq data to reference genome for splice junction discovery.
Features of MapSplice include1. alignment of both short reads < 75bp and long reads >= 75bp.2. both CPU and memory efficiency.3. detection of small exons.4. discovery of canonical, semi-canonical and non-canonical junctions.5. splice inference based on the alignment quality and diversity of reads mapped to a junction.6. identification of chimeric events (intra-chromosomes and inter-chromosomes, inter-strands) with long reads.7. support paired-end reads and single-end reads