The recent technological advances in next generation sequencing have brought the field closer to the goal of reconstructing all genomes within a community by presenting high throughput sequencing at much lower costs. While these next-generation sequencing technologies have allowed a massive increase in available raw sequence data, there are a number of new informatics challenges and difficulties that must be addressed to improve the current state.
Demultiplexing is a key step in many sequencing based applications, but it isn't always necessary as the newer Illumina pipeline software provides demultiplexed data as a standard.
Quality control is part of the data processing pipeline, since we don’t really know if an experiment has worked until the reads are aligned. Most NGS problems are diagnosed through data analysis.
In order to inspect the alignments produced we need a set of visualization tools which includes but are not limited to alignment viewers, genome browsers, etc.