The CGAT code collection has grown out of the work in comparative genomics by the Ponting group in the last decade. Now, CGAT has added functionality to do next-generation sequencing analysis.
The CGAT Code collection has two components. The first component is a collection of scripts, the CGAT tools. The second component is a collection of pipelines. While both components are part of this collection, we are currently concentrating on publishing the CGAT tools.
For questions, please subscribe and contact us at the CGAT user group.
Documentation of CGAT tools is available here.
The CGAT tools can be installed from pypi:
pip install cgat
To use CGAT Tools, use the cgat front-end. For example, to
strip sequence and quality information from a bam file, type:
cgat bam2bam --strip=sequence < in.bam > out.bam
We have developed numerous pipelines in comparative genomics and NGS analysis. The pipelines are generally available and should be fairly portable. Some documentation of the pipelines is here.
Note that we currently are not able to fully support and document the pipelines. They are under continuous development and changing rapidly. However, they might give some ideas or building blocks when developing your own pipelines.