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Python application for "Experimental High Throughput Sequencing"
High Throughput Sequencing is often conducted within an "Experimental" framework, meaning multiple samples are sequenced within a single experiment and should be processed in an identicle manner. expHTS facilities this by processing multiple samples within a single frame work and generating output so that sample quality can be easily compared across experiment samples. The first sub-application associated with expHTS is sample preprocessing. The pipeline processes RawData in the following manner:
- Screen for contaminants (minimally PhiX) Using a mapping based approach
- Deduplicate Reads Using Super-Deduper
- Quality Trimming (polyA/T) trimming Using Scickle
- Overlap paired-end reads Using Flash2
- Modify read names, filter for too-short, QA
- Produce multi-sample reports