OLego, A Sensitive Splice Mapper
OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a multiple-seed-and-extend scheme and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by using very small seeds (12–14 nt), efficiently mapped using the Burrows-Wheeler transform (BWT) and FM-index. This approach also makes it particularly sensitive for discovering small exons. OLego is implemented in C++ with full support for multithreading, enabling fast processing of large-scale data.
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SpliceTrap, A Splicing Quantification Tool
SpliceTrap is a statistical tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications in the study of alternative splicing. SpliceTrap estimates exon inclusion levels using a Bayesian inference approach. For each exon, it quantifies the extent to which it is included, skipped, or affected by size variations due to alternative 3’/5’ splice sites or intron retention. Additionally, SpliceTrap can quantify alternative splicing within a single cellular condition, without requiring a background set of reads.
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