iReckon is an algorithm for the simultaneous isoform reconstruction and abundance estimation. In addition to modelling novel isoforms, multi-mapped reads and read duplicates, this method takes into account the possible presence of unspliced pre-mRNA and intron retention. iReckon only requires a set of transcription start and end sites, but can use known full isoforms to improve sensitivity. Starting from the set of nearly all possible isoforms, iReckon uses a regularized EM algorithm to determine those actually present in the sequenced sample, together with their abundances. iReckon is multi-threaded to increase efficiency in all its time consuming steps.
Latest version of iReckon (1.0.8 final beta) is out!
It features tens of improvements and bug fixes thanks to users suggestions. Added the option of disabling novel isoform discovery.
For inqueries regarding the formats accepted by iReckon, you can check the example files describing all possibilities for the annotation file and reads files.
iReckon paper has been accepted in Genome Research journal.
Please contact ireckon ]at[ cs ]dot[ toronto dot edu for any comments/questions.
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