The PARA-suite: PAR-CLIP specific sequence read simulation and processing.

Abstract

Next-generation sequencing technologies have profoundly impacted biology over recent years. Experimental protocols, such as photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP), which identifies protein-RNA interactions on a genome-wide scale, commonly employ deep sequencing. With PAR-CLIP, the incorporation of photoactivatable nucleosides into nascent transcripts leads to high rates of specific nucleotide conversions during reverse transcription. So far, the specific properties of PAR-CLIP-derived sequencing reads have not been assessed in depth. [Source code of the PARA-suite toolkit and the PARA-suite aligner (BWA PARA) are available at https://github.com/akloetgen/PARA-suite and https://github.com/akloetgen/PARA-suite_aligner , respectively, under the GNU GPLv3 license.]