bpp-seq-omics Documentation

The bpp-seq-omics library adds 'omics' components to the bpp-seq library. These components notably include the bpp::SequenceFeature class, for storing generic sequence features and their coordinates. Parsers are provided for loading such features from a bpp::Gff file for instance, as well as tools for extracting the corresponding sequences (bpp::SequenceFeatureTools).

Next-Generation Sequencing data are also supported, with the bpp::Fastq parser, which instanciates bpp::SequenceWithQuality objects. Genome alignments can be efficiently analyzed via the bpp::MafParser class and a large range of bpp::MafIterator classes. Genome alignment blocks are stored in bpp::MafBlock instances, which are containers of bpp::MafSequence objects with their corresponding genome coordinates.