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GenOO-HTS [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-HTS is to make simple HTS analyses easy and complicated analyses possible. GenOO-HTS models biological entities into Perl objects and provides relevant attributes and methods that allow for the manipulation of high throughput sequencing data. Using GenOO-HTS as a core development module reduces the overhead and complexity of managing the data and the biological entities at hand. GenOO-HTS has been designed to be flexible, easily extendable with modular structure and minimal requirements for external tools and libraries.
Features
- 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
Project Samples
