Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data

By Sonja Althammer, Juan González-Vallinas, Cecilia Ballaré, Miguel Beato, Eduardo Eyras. Bioinform., 2011

367 citations recorded by the source corpus.

Motivation: High-throughput sequencing (HTS) has revolutionized gene regulation studies and is now fundamental for the detection of protein–DNA and protein–RNA binding, as well as for measuring RNA expression. With increasing variety and sequencing depth of HTS datasets, the need for more flexible and memory-efficient tools to analyse them is growing. Results: We describe Pyicos, a powerful toolkit for the analysis of mapped reads from diverse HTS experiments: ChIP-Seq, either punctuated or broad signals, CLIP-Seq and RNA-Seq. We prove the effectiveness of Pyicos to select for significant signals and show that its accuracy is comparable and sometimes superior to that of methods specifically designed for each particular type of experiment. Pyicos facilitates the analysis of a variety of HTS datatypes through its flexibility and memory efficiency, providing a useful framework for data integration into models of regulatory genomics. Availability: Open-source software, with tutorials and protocol files, is available at http://regulatorygenomics.upf.edu/pyicos or as a Galaxy server at http://regulatorygenomics.upf.edu/galaxy Contact: eduardo.eyras@upf.edu Supplementary Information: Supplementary data are available at Bioinformatics online.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ac86d52574b851c72a8b6671e4947e2920991605

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In Molecular Biology

Citations in the corpus

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives (2013, methodology): “Another SR-based tool, Alignment with Gap Excision (AGE), identifies SV breakpoints with base pair accuracy using more strict alignments with gap excision [23].”
DELLY: structural variant discovery by integrated paired-end and split-read analysis (2012, methodology): “…(Abyzov et al., 2011; Campbell et al., 2008; Chiang et al., 2009), split-read analysis that evaluates gapped sequence alignments to detect SVs (Abyzov and Gerstein, 2011; Wang et al., 2011; Ye et al., 2009) and sequence assembly that enables the discovery of novel sequence insertions…”
Comparative genomics reveals insights into avian genome evolution and adaptation (2014, methodology): “The alignments were generated using the Satsuma Synteny program (124), and were cleaned from overlapping and non-syntenic matches and finally the homologous synteny blocks (HSBs) were defined using the SyntenyTracker (125).”
Revealing protein–lncRNA interaction (2015, methodology): “PARalyzer [67], Piranha [68], wavClusteR [69], RIPSeeker [70], MiClip [71], PIPE-CLIP [72] and the Pyicoclip module of the Pyicoteo toolkit (previously called Pyicos) [73].”