Deep Sequencing Notes
These pages document notes I collected on various aspects of deep sequencing, aka sequencing by synthesis or short fragment sequencing. The machine on which my experience is based is a Illumina/Solexa technologies Genome Analyzer II. The work I performed was related to the deep sequencing facility in Basel (at ETH Zurich) and these are some extra-curricular notes that remain otherwise unused.
We collected some notes on compiling the pipeline v0.3 and v1.0
One of the initial aspects of Deep Sequencing is the question whether
there is a bias present and what types of biases are known.
One of the biggest problems with the software associated with the genome analyzer is that it relies on the known genome to decide on the quality of the reads. This process will even modify the quality values of the different reads. This then leads to a number of quality reports based on the alignments. We present two examples here. The first quality report is based on the eland aligner (quality report). The second quality report is based on the phage-align aligner. The output of the GA Pipeline is discussed in detail at the file formats page.
Our own software