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The PARA-suite: PAR-CLIP specific sequence read simulation and processing.
Kloetgen, Andreas Borkhardt, Arndt Hoell, Jessica I McHardy, Alice C
Kloetgen, Andreas
Borkhardt, Arndt
Hoell, Jessica I
McHardy, Alice C
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2016 (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.)
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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.]
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The PARA-suite: PAR-CLIP specific sequence read simulation and processing. 2016, 4:e2619 PeerJ
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