GenOO

GenOO: A Modern Perl Framework for High Throughput Sequencing analysis

GitHub link
Full Text Publication BioArxiv

Summary

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.

Focus

  • 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.