The ABCC supports several nextgen sequencing platforms, each with multiple applications.As part of this effort, the ABCC has collected and developed a substantial collection of software tools for nextgen sequence analyses ranging from quality assessment to de novo assembly tools and applications. The list of nextgen software tools is organized by categories of applications including assemblers, mappers, variation identification tools, mutant impact assessment tools and visualization tools, amongst others.
Nextgen sequence analysis is arbitrarily divided into primary, secondary and tertiary analysis stages. The primary analysis includes base calling and quality assessment on the different platforms as well as mapping the reads to a reference genome. Subsequent secondary analysis includes identification of variants, identification of differentially expressed messages and other application dependent related functionalities derived from the mapping data produced during the primary analysis.
Our approach to providing nextgen analysis is intended to maximize code-reuse and other efficiencies while providing comprehensive support to this growing technology. Logistically, this includes teams tasked with production of primary data and migration of that data, providing hands-on collaborative detailed analysis and also a technology development team that makes iterative improvements to the tool palette available to both the analysts and the larger community.
Because many of the nextgen data files are extremely large, access to both the data and the associated tools is facilitated through access to the ABCC data center servers. Information regarding obtaining an account can be found at this link
The ABCC has developed a number of views into the rapidly evolving NextGen Sequencing arena:
Workflows – detailed descriptions of our current and “to-be” workflows for various nextgen applications
External Resources – descriptions and links to external nextgen sources