Category Archives: Current

CLIP Seq Tools

GitHub link
CPAN link


CLIPSeqTools is a collection of command line applications used for the analysis of CLIP-Seq (UV cross-linking and immunoprecipitation with high-throughput sequencing) data. It offers a wide range of analyses (eg. genome read coverage, motif enrichment, relative positioning of reads of two libraries, etc). The toolbox is primarily oriented for bioinformaticians but the commands are simple enough for non experts to use.


GenOO: A Modern Perl Framework for High Throughput Sequencing analysis

GitHub link
Full Text Publication BioArxiv


GenOO [jee-noo] is an open-source; object-oriented Perl framework specifically developed for the design of High Throughput Sequencing (HTS) analysis tools. The primary aim of GenOO is to make simple HTS analyses easy and complicated analyses possible. GenOO models biological entities into Perl objects and provides relevant attributes and methods that allow for the manipulation of high throughput sequencing data. Using GenOO as a core development module reduces the overhead and complexity of managing the data and the biological entities at hand. GenOO has been designed to be flexible, easily extendable with modular structure and minimal requirements for external tools and libraries.


  • Organize biological entities as perl objects (genomic regions, genes, transcripts, introns/exons, etc)
  • Organize sequencing entities as perl objects/attributes (sequencing reads, alignments, etc)
  • Make I/O from widely used file formats easy (SAM, BED, FASTA, FASTQ)
  • Be consistent and easily extendable

We want to keep this framework focused on the real issues found in sequencing analyses and balance being easily extendable with being focused and efficient.